Combinatorial oligomer immunoabsorbant screening assay for transcription factors and other biomolecule binding

Claim 1

A method for determining the sequence of an oligonucleotide having specific binding activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. modifying the oligonucleotides of the sets of oligonucleotides with linker moieties for attaching the oligonucleotides to a solid support; (b) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (c) attaching the sets of oligonucleotides to a solid support via the linker moiety; (d) separating bound from unbound transcription factor; (e) detecting the binding of transcription factor to each set of oligonucleotides attached to solid support where greatest binding is indicative of highest specific binding activity; (f) selecting the set having the highest activity; (g) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (h) modifying the oligonucleotides of the sets of oligonucleotides with linker moieties for attaching the oligonucleotides to a solid support; (i) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (j) attaching the sets of oligonucleotides to a solid support via the linker moiety; (k) separating bound from unbound transcription factor; (l) detecting the binding of transcription factor to each set of oligonucleotides attached to solid support where greatest binding is indicative of highest specific binding activity; (m) selecting the set having the highest activity; and (n) performing steps (g) through (m) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 2

A method for determining the sequence of an oligonucleotide having specific binding activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. modifying the oligonucleotides of the sets of oligonucleotides with linker moieties for attaching the oligonucleotides to a solid support; (b) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (c) attaching the sets of oligonucleotides to a solid support via the linker moiety; (d) separating bound from unbound transcription factor; (e) detecting the binding of transcription factor to each set of oligonucleotides attached to solid support where greatest binding is indicative of highest specific binding activity; (f) selecting the set having the highest activity; (g) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (h) modifying the oligonucleotides of the sets of oligonucleotides with linker moieties for attaching the oligonucleotides to a solid support; (i) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (j) attaching the sets of oligonucleotides to a solid support via the linker moiety; (k) separating bound from unbound transcription factor; (l) detecting the binding of transcription factor to each set of oligonucleotides attached to solid support where greatest binding is indicative of highest specific binding activity; (m) selecting the set having the highest activity; and (n) performing steps (g) through (m) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 10

A method for determining the sequence of an oligonucleotide having specific binding activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. detectably labeling oligonucleotides of each set of oligonucleotides; (b) modifying the transcription factor with a linker moiety for attaching the transcription factor to a solid support; (c) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (d) attaching the transcription factor to a solid support via the linker moiety; (e) separating bound from unbound oligonucleotide; (f) detecting the binding of each oligonucleotide set to the transcription factor attached to solid support where greatest binding is indicative of highest specific binding activity; (g) selecting the set having the highest activity; (h) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (i) detectably labeling oligonucleotides of each set of oligonucleotides; (j) modifying the transcription factor with a linker moiety for attaching the transcription factor to a solid support; (k) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (l) attaching the transcription factor to a solid support via the linker moiety; (m) separating bound from unbound oligonucleotide; (n) detecting the binding of each oligonucleotide set to transcription factor attached to solid support where greatest binding is indicative of highest specific binding activity; (o) selecting the set having the highest activity; and (p) performing steps (h) through (o) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 11

A method for determining the sequence of an oligonucleotide having specific binding activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. detectably labeling oligonucleotides of each set of oligonucleotides; (b) modifying the transcription factor with a linker moiety for attaching the transcription factor to a solid support; (c) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (d) attaching the transcription factor to a solid support via the linker moiety; (e) separating bound from unbound oligonucleotide; (f) detecting the binding of each oligonucleotide set to the transcription factor attached to solid support where greatest binding is indicative of highest specific binding activity; (g) selecting the set having the highest activity; (h) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (i) detectably labeling oligonucleotides of each set of oligonucleotides; (j) modifying the transcription factor with a linker moiety for attaching the transcription factor to a solid support; (k) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (l) attaching the transcription factor to a solid support via the linker moiety; (m) separating bound from unbound oligonucleotide; (n) detecting the binding of each oligonucleotide set to transcription factor attached to solid support where greatest binding is indicative of highest specific binding activity; (o) selecting the set having the highest activity; and (p) performing steps (h) through (o) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 19

A method for determining the sequence of an oligonucleotide having specific binding activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) modifying the transcription factor with a linker moiety for attaching the transcription factor to a solid support; (c) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (d) adding a competitor under binding conditions to form transcription factor-competitor complexes; (e) attaching the transcription factor to a solid support via the linker moiety; (f) separating bound from unbound competitor; (g) detecting the binding of the competitor to the transcription factor attached to solid support where lowest binding is indicative of highest oligonucleotide specific binding activity; (h) selecting the set having the highest activity; (i) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (j) modifying the transcription factor with a linker moiety for attaching the transcription factor to a solid support; (k) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (l) adding the competitor under binding conditions to form transcription factor-competitor complexes; (m) attaching the transcription factor to a solid support via the linker moiety; (n) separating bound from unbound competitor; (o) detecting the binding of the competitor to the transcription factor attached to solid support where lowest binding is indicative of highest oligonucleotide specific binding activity; (p) selecting the set having the highest activity; and (q) performing steps (i) through (p) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 20

A method for determining the sequence of an oligonucleotide having specific binding activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) modifying the transcription factor with a linker moiety for attaching the transcription factor to a solid support; (c) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (d) adding a competitor under binding conditions to form transcription factor-competitor complexes; (e) attaching the transcription factor to a solid support via the linker moiety; (f) separating bound from unbound competitor; (g) detecting the binding of the competitor to the transcription factor attached to solid support where lowest binding is indicative of highest oligonucleotide specific binding activity; (h) selecting the set having the highest activity; (i) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (j) modifying the transcription factor with a linker moiety for attaching the transcription factor to a solid support; (k) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (l) adding the competitor under binding conditions to form transcription factor-competitor complexes; (m) attaching the transcription factor to a solid support via the linker moiety; (n) separating bound from unbound competitor; (o) detecting the binding of the competitor to the transcription factor attached to solid support where lowest binding is indicative of highest oligonucleotide specific binding activity; (p) selecting the set having the highest activity; and (q) performing steps (i) through (p) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 27

A method for determining the sequence of an oligonucleotide having specific activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) preparing a competitor modified with a linker moiety for attaching the competitor to a solid support; (c) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (d) adding a competitor under binding conditions to form transcription factor-competitor complexes; (e) attaching the competitor to a solid support via the linker moiety; (f) separating bound from unbound transcription factor; (g) detecting binding of the transcription factor bound to the competitor where lowest binding is indicative of highest oligonucleotide specific binding activity; (h) selecting the set having the highest activity; (i) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (j) preparing the competitor modified with a linker moiety for attaching the competitor to a solid support; (k) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (l) adding the competitor under binding conditions to form transcription factor-competitor complexes; (m) attaching the competitor to a solid support via the linker moiety; (n) separating bound from unbound transcription factor; (o) detecting binding of the transcription factor to the competitor where lowest binding is indicative of highest oligonucleotide specific binding activity; (p) selecting the set having the highest activity; and (q) performing steps (i) through (p) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 28

A method for determining the sequence of an oligonucleotide having specific activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) preparing a competitor modified with a linker moiety for attaching the competitor to a solid support; (c) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (d) adding a competitor under binding conditions to form transcription factor-competitor complexes; (e) attaching the competitor to a solid support via the linker moiety; (f) separating bound from unbound transcription factor; (g) detecting binding of the transcription factor bound to the competitor where lowest binding is indicative of highest oligonucleotide specific binding activity; (h) selecting the set having the highest activity; (i) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (j) preparing the competitor modified with a linker moiety for attaching the competitor to a solid support; (k) incubating each of said sets of oligonucleotides with the transcription factor under binding conditions to form oligonucleotide-transcription factor complexes; (l) adding the competitor under binding conditions to form transcription factor-competitor complexes; (m) attaching the competitor to a solid support via the linker moiety; (n) separating bound from unbound transcription factor; (o) detecting binding of the transcription factor to the competitor where lowest binding is indicative of highest oligonucleotide specific binding activity; (p) selecting the set having the highest activity; and (q) performing steps (i) through (p) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 35

A method for determining the sequence of an oligonucleotide having specific activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) modifying a first competitor with a linker moiety for attaching the first competitor to a solid support; (c) incubating the transcription factor and the first competitor under binding conditions to form transcription factor-competitor complexes; (d) incubating each of the sets of oligonucleotides with the transcription factor-competitor complex under binding conditions to form oligonucleotide-transcription factor-competitor complexes; (e) adding a second competitor under binding conditions to form further complexes; (f) attaching the first competitor to a solid support via the linker moiety; (g) separating bound from unbound second competitor; (h) detecting binding of the second competitor to the transcription factor where lowest binding is indicative of highest oligonucleotide specific binding activity; (i) selecting the set having the highest activity; (j) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (k) modifying the first competitor with a linker moiety for attaching the first competitor to a solid support; (l) incubating the transcription factor and the first competitor under binding conditions to form transcription factor-competitor complexes; (m) incubating each of the sets of oligonucleotides with the transcription factor-competitor complexes under binding conditions to form oligonucleotide-transcription factor-competitor complexes; (n) adding the second competitor under binding conditions to form further complexes; (o) attaching the first competitor to a solid support via the linker moiety; (p) separating bound from unbound second competitor; (q) detecting binding of the second competitor to the transcription factor where lowest binding is indicative of highest oligonucleotide specific binding activity; (r) selecting the set having the highest activity; and (s) performing steps (j) through (r) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 36

A method for determining the sequence of an oligonucleotide having specific activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) modifying a first competitor with a linker moiety for attaching the first competitor to a solid support; (c) incubating the transcription factor and the first competitor under binding conditions to form transcription factor-competitor complexes; (d) incubating each of the sets of oligonucleotides with the transcription factor-competitor complex under binding conditions to form oligonucleotide-transcription factor-competitor complexes; (e) adding a second competitor under binding conditions to form further complexes; (f) attaching the first competitor to a solid support via the linker moiety; (g) separating bound from unbound second competitor; (h) detecting binding of the second competitor to the transcription factor where lowest binding is indicative of highest oligonucleotide specific binding activity; (i) selecting the set having the highest activity; (j) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (k) modifying the first competitor with a linker moiety for attaching the first competitor to a solid support; (l) incubating the transcription factor and the first competitor under binding conditions to form transcription factor-competitor complexes; (m) incubating each of the sets of oligonucleotides with the transcription factor-competitor complexes under binding conditions to form oligonucleotide-transcription factor-competitor complexes; (n) adding the second competitor under binding conditions to form further complexes; (o) attaching the first competitor to a solid support via the linker moiety; (p) separating bound from unbound second competitor; (q) detecting binding of the second competitor to the transcription factor where lowest binding is indicative of highest oligonucleotide specific binding activity; (r) selecting the set having the highest activity; and (s) performing steps (j) through (r) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 41

A method for determining the sequence of an oligonucleotide having specific activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. detectably labeling oligonucleotides of each set of oligonucleotides; (b) modifying a first competitor with a linker moiety for attaching the first competitor to a solid support; (c) incubating the transcription factor and the first competitor under binding conditions to form transcription factor-competitor complexes; (d) incubating each of the sets of oligonucleotides with the transcription factor-competitor complex under binding conditions to form oligonucleotide-transcription factor-competitor complexes; (e) adding a second competitor under binding conditions to form further complexes; (f) attaching the first competitor to a solid support via the linker moiety; (g) separating bound from unbound second competitor; (h) detecting binding of the oligonucleotide to the transcription factor where highest binding is indicative of highest oligonucleotide specific binding activity; (i) selecting the set having the highest activity; (j) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (k) detectably labeling oligonucleotides of each set of oligonucleotides; (l) modifying the first competitor with a linker moiety for attaching the first competitor to a solid support; (m) incubating the transcription factor and the first competitor under binding conditions to form transcription factor-competitor complexes; (n) incubating each of the sets of oligonucleotides with the transcription factor-competitor complexes under binding conditions to form oligonucleotide-transcription factor-competitor complexes; (o) adding the second competitor under binding conditions to form further complexes; (p) attaching the first competitor to a solid support via the linker moiety; (q) separating bound from unbound second competitor; (r) detecting binding of the oligonucleotide to the transcription factor where highest binding is indicative of highest oligonucleotide specific binding activity; (s) selecting the set having the highest activity; and (t) performing steps (j) through (s) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 42

A method for determining the sequence of an oligonucleotide having specific activity for a transcription factor comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. detectably labeling oligonucleotides of each set of oligonucleotides; (b) modifying a first competitor with a linker moiety for attaching the first competitor to a solid support; (c) incubating the transcription factor and the first competitor under binding conditions to form transcription factor-competitor complexes; (d) incubating each of the sets of oligonucleotides with the transcription factor-competitor complex under binding conditions to form oligonucleotide-transcription factor-competitor complexes; (e) adding a second competitor under binding conditions to form further complexes; (f) attaching the first competitor to a solid support via the linker moiety; (g) separating bound from unbound second competitor; (h) detecting binding of the oligonucleotide to the transcription factor where highest binding is indicative of highest oligonucleotide specific binding activity; (i) selecting the set having the highest activity; (j) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (k) detectably labeling oligonucleotides of each set of oligonucleotides; (l) modifying the first competitor with a linker moiety for attaching the first competitor to a solid support; (m) incubating the transcription factor and the first competitor under binding conditions to form transcription factor-competitor complexes; (n) incubating each of the sets of oligonucleotides with the transcription factor-competitor complexes under binding conditions to form oligonucleotide-transcription factor-competitor complexes; (o) adding the second competitor under binding conditions to form further complexes; (p) attaching the first competitor to a solid support via the linker moiety; (q) separating bound from unbound second competitor; (r) detecting binding of the oligonucleotide to the transcription factor where highest binding is indicative of highest oligonucleotide specific binding activity; (s) selecting the set having the highest activity; and (t) performing steps (j) through (s) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the transcription factor has been determined.

Claim 47

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. modifying the oligonucleotides of the sets of oligonucleotides with linker moieties for attaching the oligonucleotides to a solid support; (b) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (c) attaching the sets of oligonucleotides to a solid support via the linker moiety; (d) separating bound from unbound target molecule; (e) detecting the binding of target molecule to each set of oligonucleotides attached to solid support where greatest binding is indicative of highest specific binding activity; (f) selecting the set having the highest activity; (g) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (h) modifying the oligonucleotides of the sets of oligonucleotides with linker moieties for attaching the oligonucleotides to a solid support; (i) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (j) attaching the sets of oligonucleotides to a solid support via the linker moiety; (k) separating bound from unbound target molecule; (l) detecting the binding of target molecule to each set of oligonucleotides attached to solid support where greatest binding is indicative of highest specific binding activity; (m) selecting the set having the highest activity; and (n) performing steps (g) through (m) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 48

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. modifying the oligonucleotides of the sets of oligonucleotides with linker moieties for attaching the oligonucleotides to a solid support; (b) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (c) attaching the sets of oligonucleotides to a solid support via the linker moiety; (d) separating bound from unbound target molecule; (e) detecting the binding of target molecule to each set of oligonucleotides attached to solid support where greatest binding is indicative of highest specific binding activity; (f) selecting the set having the highest activity; (g) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (h) modifying the oligonucleotides of the sets of oligonucleotides with linker moieties for attaching the oligonucleotides to a solid support; (i) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (j) attaching the sets of oligonucleotides to a solid support via the linker moiety; (k) separating bound from unbound target molecule; (l) detecting the binding of target molecule to each set of oligonucleotides attached to solid support where greatest binding is indicative of highest specific binding activity; (m) selecting the set having the highest activity; and (n) performing steps (g) through (m) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 53

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. detectably labeling oligonucleotides of each set of oligonucleotides; (b) modifying the target molecule with a linker moiety for attaching the target molecule to a solid support; (c) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (d) attaching the target molecule to a solid support via the linker moiety; (e) separating bound from unbound oligonucleotide; (f) detecting the binding of each oligonucleotide set to the target molecule attached to solid support where greatest binding is indicative of highest specific binding activity; (g) selecting the set having the highest activity (h) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (i) detectably labeling oligonucleotides of each set of oligonucleotides; (j) modifying the target molecule with a linker moiety for attaching the target molecule to a solid support; (k) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (l) attaching the target molecule to a solid support via the linker moiety; (m) separating bound from unbound oligonucleotide; (n) detecting the binding of each oligonucleotide set to target molecule attached to solid support where greatest binding is indicative of highest specific binding activity; (o) selecting the set having the highest activity; and (p) performing steps (h) through (o) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 54

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. detectably labeling oligonucleotides of each set of oligonucleotides; (b) modifying the target molecule with a linker moiety for attaching the target molecule to a solid support; (c) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (d) attaching the target molecule to a solid support via the linker moiety; (e) separating bound from unbound oligonucleotide; (f) detecting the binding of each oligonucleotide set to the target molecule attached to solid support where greatest binding is indicative of highest specific binding activity; (g) selecting the set having the highest activity (h) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (i) detectably labeling oligonucleotides of each set of oligonucleotides; (j) modifying the target molecule with a linker moiety for attaching the target molecule to a solid support; (k) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (l) attaching the target molecule to a solid support via the linker moiety; (m) separating bound from unbound oligonucleotide; (n) detecting the binding of each oligonucleotide set to target molecule attached to solid support where greatest binding is indicative of highest specific binding activity; (o) selecting the set having the highest activity; and (p) performing steps (h) through (o) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 59

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) modifying the target molecule with a linker moiety for attaching the target molecule to a solid support; (c) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (d) adding a competitor under binding conditions to form target-competitor complexes; (e) attaching the target molecule to a solid support via the linker moiety; (f) separating bound from unbound competitor; (g) detecting the binding of the competitor to the target molecule attached to solid support where lowest binding is indicative of highest oligonucleotide specific binding activity; (h) selecting the set having the highest activity; (i) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (j) modifying the target molecule with a linker moiety for attaching the target molecule to a solid support; (k) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (l) adding the competitor under binding conditions to form target-competitor complexes; (m) attaching the target molecule to a solid support via the linker moiety; (n) separating bound from unbound competitor; (o) detecting the binding of the competitor to the target molecule attached to solid support where lowest binding is indicative of highest oligonucleotide specific binding activity; (p) selecting the set having the highest activity; and (q) performing steps (i) through (p) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 60

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) modifying the target molecule with a linker moiety for attaching the target molecule to a solid support; (c) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (d) adding a competitor under binding conditions to form target-competitor complexes; (e) attaching the target molecule to a solid support via the linker moiety; (f) separating bound from unbound competitor; (g) detecting the binding of the competitor to the target molecule attached to solid support where lowest binding is indicative of highest oligonucleotide specific binding activity; (h) selecting the set having the highest activity; (i) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (j) modifying the target molecule with a linker moiety for attaching the target molecule to a solid support; (k) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (l) adding the competitor under binding conditions to form target-competitor complexes; (m) attaching the target molecule to a solid support via the linker moiety; (n) separating bound from unbound competitor; (o) detecting the binding of the competitor to the target molecule attached to solid support where lowest binding is indicative of highest oligonucleotide specific binding activity; (p) selecting the set having the highest activity; and (q) performing steps (i) through (p) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 64

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) preparing a competitor modified with a linker moiety for attaching the competitor to a solid support; (c) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes, (d) adding a competitor under binding conditions to form target-competitor complexes; (e) attaching the competitor to a solid support via the linker moiety; (f) separating bound from unbound target molecule; (g) detecting binding of the target molecule bound to the competitor where lowest binding is indicative of highest oligonucleotide specific binding activity; (h) selecting the set having the highest activity; (i) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (j) preparing the competitor modified with a linker moiety for attaching the competitor to a solid support; (k) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (l) adding the competitor under binding conditions to form target-competitor complexes; (m) attaching the competitor to a solid support via the linker moiety; (n) separating bound from unbound target molecule; (o) detecting binding of the target molecule to the competitor where lowest binding is indicative of highest oligonucleotide specific binding activity; (p) selecting the set having the highest activity; and (q) performing steps (i) through (p) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 65

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) preparing a competitor modified with a linker moiety for attaching the competitor to a solid support; (c) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes, (d) adding a competitor under binding conditions to form target-competitor complexes; (e) attaching the competitor to a solid support via the linker moiety; (f) separating bound from unbound target molecule; (g) detecting binding of the target molecule bound to the competitor where lowest binding is indicative of highest oligonucleotide specific binding activity; (h) selecting the set having the highest activity; (i) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (j) preparing the competitor modified with a linker moiety for attaching the competitor to a solid support; (k) incubating each of said sets of oligonucleotides with the target molecule under binding conditions to form oligonucleotide-target complexes; (l) adding the competitor under binding conditions to form target-competitor complexes; (m) attaching the competitor to a solid support via the linker moiety; (n) separating bound from unbound target molecule; (o) detecting binding of the target molecule to the competitor where lowest binding is indicative of highest oligonucleotide specific binding activity; (p) selecting the set having the highest activity; and (q) performing steps (i) through (p) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 69

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) modifying a first competitor with a linker moiety for attaching the first competitor to a solid support; (c) incubating the target molecule and the first competitor under binding conditions to form target-competitor complexes; (d) incubating each of the sets of oligonucleotides with the target-competitor complex under binding conditions to form oligonucleotide-target-competitor complexes; (e) adding a second competitor under binding conditions to form further complexes; (f) attaching the first competitor to a solid support via the linker moiety; (g) separating bound from unbound second competitor; (h) detecting binding of the second competitor to the target molecule where lowest binding is indicative of highest oligonucleotide specific binding activity; (i) selecting the set having the highest activity; (j) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common Position being randomized; (k) modifying the first competitor with a linker moiety for attaching the first competitor to a solid support; (l) incubating the target molecule and the first competitor under binding conditions to form target-competitor complexes; (m) incubating each of the sets of oligonucleotides with the target-competitor complexes under binding conditions to form oligonucleotide-target-competitor complexes; (n) adding the second competitor under binding conditions to form further complexes; (o) attaching the first competitor to a solid support via the linker moiety; (p) separating bound from unbound second competitor; (q) detecting binding of the second competitor to the target molecule where lowest binding is indicative of highest oligonucleotide specific binding activity; (r) selecting the set having the highest activity; and (s) performing steps (j) through (r) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 70

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, and ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized; (b) modifying a first competitor with a linker moiety for attaching the first competitor to a solid support; (c) incubating the target molecule and the first competitor under binding conditions to form target-competitor complexes; (d) incubating each of the sets of oligonucleotides with the target-competitor complex under binding conditions to form oligonucleotide-target-competitor complexes; (e) adding a second competitor under binding conditions to form further complexes; (f) attaching the first competitor to a solid support via the linker moiety; (g) separating bound from unbound second competitor; (h) detecting binding of the second competitor to the target molecule where lowest binding is indicative of highest oligonucleotide specific binding activity; (i) selecting the set having the highest activity; (j) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common Position being randomized; (k) modifying the first competitor with a linker moiety for attaching the first competitor to a solid support; (l) incubating the target molecule and the first competitor under binding conditions to form target-competitor complexes; (m) incubating each of the sets of oligonucleotides with the target-competitor complexes under binding conditions to form oligonucleotide-target-competitor complexes; (n) adding the second competitor under binding conditions to form further complexes; (o) attaching the first competitor to a solid support via the linker moiety; (p) separating bound from unbound second competitor; (q) detecting binding of the second competitor to the target molecule where lowest binding is indicative of highest oligonucleotide specific binding activity; (r) selecting the set having the highest activity; and (s) performing steps (j) through (r) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 75

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. detectably labeling oligonucleotides of each set of oligonucleotides; (b) modifying a first competitor with a linker moiety for attaching the first competitor to a solid support; (c) incubating the target molecule and the first competitor under binding conditions to form target-competitor complexes; (d) incubating each of the sets of oligonucleotides with the target-competitor complex under binding conditions to form oligonucleotide-target-competitor complexes; (e) adding a second competitor under binding conditions to form further complexes; (f) attaching the first competitor to a solid support via the linker moiety; (g) separating bound from unbound second competitor; (h) detecting binding of the oligonucleotide to the target molecule where highest binding is indicative of highest oligonucleotide specific binding activity; (i) selecting the set having the highest activity; (j) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (k) detectably labeling oligonucleotides of each set of oligonucleotides; (l) modifying the first competitor with a linker moiety for attaching the first competitor to a solid support; (m) incubating the target molecule and the first competitor under binding conditions to form target-competitor complexes; (n) incubating each of the sets of oligonucleotides with the target-competitor complex under binding conditions to form oligonucleotide-target-competitor complexes; (o) adding the second competitor under binding conditions to form further complexes; (p) attaching the first competitor to a solid support via the linker moiety; (q) separating bound from unbound second competitor; (r) detecting binding of the oligonucleotide to the target molecule where highest binding is indicative of highest oligonucleotide specific binding activity; (s) selecting the set having the highest specific binding activity; and (t) performing steps (j) through (s) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.

Claim 76

A method for determining the sequence of an oligonucleotide having specific activity for a target molecule comprising the steps of: (a) preparing a group comprising a plurality of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotides, by: i. defining a common position in the oligonucleotides of the sets, ii. synthesizing said sets of oligonucleotides such that each set has a different nucleotide in said common position, the nucleotides which are not in said common position being randomized, and iii. detectably labeling oligonucleotides of each set of oligonucleotides; (b) modifying a first competitor with a linker moiety for attaching the first competitor to a solid support; (c) incubating the target molecule and the first competitor under binding conditions to form target-competitor complexes; (d) incubating each of the sets of oligonucleotides with the target-competitor complex under binding conditions to form oligonucleotide-target-competitor complexes; (e) adding a second competitor under binding conditions to form further complexes; (f) attaching the first competitor to a solid support via the linker moiety; (g) separating bound from unbound second competitor; (h) detecting binding of the oligonucleotide to the target molecule where highest binding is indicative of highest oligonucleotide specific binding activity; (i) selecting the set having the highest activity; (j) preparing a further group comprising a plurality of sets of oligonucleotides, each of the sets having in the previous common position the nucleotide appearing in the previously defined common position in the selected one of the previous group of sets; each set of said further group of sets having a different nucleotide in an additional common position, the nucleotides in the position of the oligonucleotide which are not in a common position being randomized; (k) detectably labeling oligonucleotides of each set of oligonucleotides; (l) modifying the first competitor with a linker moiety for attaching the first competitor to a solid support; (m) incubating the target molecule and the first competitor under binding conditions to form target-competitor complexes; (n) incubating each of the sets of oligonucleotides with the target-competitor complex under binding conditions to form oligonucleotide-target-competitor complexes; (o) adding the second competitor under binding conditions to form further complexes; (p) attaching the first competitor to a solid support via the linker moiety; (q) separating bound from unbound second competitor; (r) detecting binding of the oligonucleotide to the target molecule where highest binding is indicative of highest oligonucleotide specific binding activity; (s) selecting the set having the highest specific binding activity; and (t) performing steps (j) through (s) iteratively until the sequence of at least one oligonucleotide having specific binding activity for the target molecule has been determined.