US5082767A
Expired / Lapsed
US
⏱️ 0.0 years remaining
Codon pair utilization
Assignee: University of California
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Filing: 1989-02-27
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Granted: 1992-01-21
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Expires: 2009-02-27
Abstract
Abstract A method for determining the pattern of nonrandom codon pair usage of an organism, comprising the steps of obtaining nucleotide sequence data for the organism, determining from the data the number of codons represented in at least a portion of the sequence and the frequency of usage of at least some codons in the portion, determining from the frequency the expected number of occurrences of at least some codon pairs, if they are paired in a random manner, and comparing the expected number with the actual number of occurrences to determine relative codon pairing preferences. The codon pairings of organisms are highly nonrandom, and differ from organism to organism. This information is used to construct and express altered or synthetic genes having desired levels of translational efficiency, to determine which regions in a genome are protein coding regions, to introduce translational pause sites into heterologous genes, and to ascertain relationship or ancestral origin of nucleotide sequences.
Inventors
- 👤 G. Wesley Hatfield
- 👤 George A. Gutman
Bibliographic Details
Application Number
—
Jurisdiction
US
Data Source
google_patents
Last Synchronized
2026-11-04 16:03
CPC Classifications
C; C12; C12Q; C12Q1/00; C12Q1/68; C07; C07K; C07K1/00; C07K1/107; C07K1/113; C07K1/1136; C12Q1/6876; C12Q1/6888; C12Q2600/00; C12Q2600/158
Claims Analysis
Total Claims: 55
Claim 1
Independent Claim
164 words
A method for determining relative native codon pairing preferences in an organism, comprising the steps of: obtaining nucleotide sequence data for said organism; determining from said data the number of codons represented in at least a portion of said sequence and the frequency of usage of at least some individual codons in said portion; determining from said individual codon frequencies the expected number of occurrences of at least some codon pairs, if said codons are paired in a radon manner; comparing the expected number with the actual number of occurrences to determine said relative condon pairing preferences; determining preferred amino acid pairings of said organism and eliminating any amino acid pair bias prior to determining said codon pairing preferences; and altering a gene for expression in said organism by substituting at least one codon for an existing codon in said gene to alter codon pairing in accordance with said codon pairing preferences to change the translational kinetics of said gene in a predetermined manner.
Claim 2
Independent Claim
164 words
A method for determining relative native codon pairing preferences in an organism, comprising the steps of: obtaining nucleotide sequence data for said organism; determining from said data the number of codons represented in at least a portion of said sequence and the frequency of usage of at least some individual codons in said portion; determining from said individual codon frequencies the expected number of occurrences of at least some codon pairs, if said codons are paired in a radon manner; comparing the expected number with the actual number of occurrences to determine said relative condon pairing preferences; determining preferred amino acid pairings of said organism and eliminating any amino acid pair bias prior to determining said codon pairing preferences; and altering a gene for expression in said organism by substituting at least one codon for an existing codon in said gene to alter codon pairing in accordance with said codon pairing preferences to change the translational kinetics of said gene in a predetermined manner.
Claim 3
Dependent Claim
25 words
The method of claim 1, in which said codon pairing is altered to increase the translational kinetics of at least a portion of said gene.
Claim 4
Dependent Claim
40 words
The method of claim 2, in which said codon pairing is altered to increase the number of codon pairs that, in comparison to random codon pair usage, are the more abundant and yet more under-represented codon pairs in said organism.
Claim 5
Dependent Claim
25 words
The method of claim 1, in which said codon pairing is altered to decrease the translational kinetics of at least a portion of said gene.
Claim 6
Dependent Claim
40 words
The method of claim 4, in which said codon pairing is altered to increase the number of codon pairs that, in comparison to random codon pair usage, are the less abundant and yet more over-represented codon pairs in said organism.
Claim 7
Dependent Claim
16 words
The method of claim 1, wherein at least 100% of the existing condons pairs are changed.
Claim 8
Dependent Claim
56 words
The method of claim 1, further comprising the step of constructing a synthetic gene coding for a predetermined polypeptide for expression in said organism, and selecting codons for amino acids of said polypeptide in accordance with the relative native condon pairing preferences of said organism to achieve a desired level of translational kinetics of said gene.
Claim 9
Dependent Claim
27 words
The method of claim 7, wherein at least 10% of said codon pairs are selected in accordance with the relative native codon pairing preferences of said organism.
Claim 10
Dependent Claim
34 words
The method of claim 7, in which said codon pairing is selected to increase the number of codon pairs that, in comparison to random codon pair usage, are underepresented codon pairs in said organism.
Claim 11
Dependent Claim
34 words
The method of claim 7, in which said codon pairing is selected to increase the number of codon pairs that, in comparison to random codon pair usage, are over-represented codon pairs in said organism.
Claim 12
Independent Claim
84 words
A method for making at least a portion of a synthetic gene coding for a polypeptide, wherein said gene is intended for expression in a particular organism, comprising the steps of: obtaining information regarding the relationship between codon pairing and translational kinetics for said organism; and for at least one amino acid pair in said polypeptide, selecting from among possible codon pairs a pair that provides desired translational kinetics; and providing said selected codon pair in said gene in place of a less-preferred pair.
Claim 13
Independent Claim
84 words
A method for making at least a portion of a synthetic gene coding for a polypeptide, wherein said gene is intended for expression in a particular organism, comprising the steps of: obtaining information regarding the relationship between codon pairing and translational kinetics for said organism; and for at least one amino acid pair in said polypeptide, selecting from among possible codon pairs a pair that provides desired translational kinetics; and providing said selected codon pair in said gene in place of a less-preferred pair.
Claim 14
Dependent Claim
20 words
The method of claim 11, wherein at least three codon pairs are selected and provided in accordance with said information.
Claim 15
Dependent Claim
29 words
The method of claim 11, wherein said selected codon pair is preferred by said organism in genes expressed at low levels of less than about 1000 copies per cell.
Claim 16
Dependent Claim
31 words
The method of claim 11, wherein said selected codon pair is preferred by said organism in genes expressed at intermediate levels of from about 1000 to about 10,000 copies per cell.
Claim 17
Dependent Claim
29 words
The method of claim 11, wherein said selected codon pair is preferred by said organism in genes expressed at high levels of greater than about 10,000 copies per cell.
Claim 18
Dependent Claim
19 words
The method of claim 11, wherein said selecting step affects at least 10% of the codons of said gene.
Claim 19
Independent Claim
94 words
A method for altering a gene of a first organism for expression in a second organism, comprising the steps of: obtaining information regarding native codon pairing preferences for at least some genes of said second organism; and replacing one or more existing codon pairs of said gene of said first organism in accordance with said information with codon pairs coding for the same amino acids but for which said second organism has different preferences that it does for said existing codon pairs, to alter the translational kinetics of said pairs in a predetermined manner.
Claim 20
Independent Claim
94 words
A method for altering a gene of a first organism for expression in a second organism, comprising the steps of: obtaining information regarding native codon pairing preferences for at least some genes of said second organism; and replacing one or more existing codon pairs of said gene of said first organism in accordance with said information with codon pairs coding for the same amino acids but for which said second organism has different preferences that it does for said existing codon pairs, to alter the translational kinetics of said pairs in a predetermined manner.
Claim 21
Dependent Claim
42 words
The method of claim 17, wherein said replacing step alters at least one codon pair to a pair over-represented or under-represented in said genes of said second organism to the same general degree as was said replaced pair in said first organism.
Claim 22
Dependent Claim
17 words
The method of claim 17, wherein said replacing step increases the translational speed of said codon pairs.
Claim 23
Dependent Claim
17 words
The method of claim 17, wherein said replacing step decreases the translational speed of said codon pairs.
Claim 24
Dependent Claim
40 words
A method for expressing a gene in an organism, said gene having altered translational kinetics, comprising the steps of: introducing a gene prepared according to the method of claim 1 into said organism; and expressing said gene in said organism.
Claim 25
Dependent Claim
40 words
A method for expressing a gene in an organism, said gene having altered translational kinetics, comprising the steps of: introducing a gene prepared according to the method of claim 7 into said organism; and expressing said gene in said organism.
Claim 26
Dependent Claim
40 words
A method for expressing a gene in an organism, said gene having altered translational kinetics, comprising the steps of: introducing a gene prepared according to the method of claim 19 into said organism; and expressing said gene in said organism.
Claim 27
Dependent Claim
36 words
A method for expressing a gene in an organism, said gene having altered translational kinetics, introducing a gene prepared according to the method of claim 20 into said organism; and expressing said gene in said organism.
Claim 28
Dependent Claim
66 words
A heterologous DNA sequence coding for a predetermined polypeptide for expression in a first organism, comprising: a plurality of codon pairs coding for amino acid pairs of acid polypeptide, wherein at least three of said pairs have been selected from among possible codon pairs to correspond to nonrandom codon pair usage patterns of genes expressed at a level within a predetermined range in said first organism.
Claim 29
Dependent Claim
66 words
A heterologous DNA sequence coding for a predetermined polypeptide for expression in a first organism, comprising: a plurality of codon pairs coding for amino acid pairs of acid polypeptide, wherein at least three of said pairs have been selected from among possible codon pairs to correspond to nonrandom codon pair usage patterns of genes expressed at a level within a predetermined range in said first organism.
Claim 30
Dependent Claim
21 words
The DNA sequence of claim 25, wherein said predetermined range of expression is levels greater than about 10,000 copies per cell.
Claim 31
Dependent Claim
21 words
The DNA sequence of claim 25, wherein said predetermined range of expression is between about 1000 and 10,000 copies per cell.
Claim 32
Dependent Claim
19 words
The DNA sequence of claim 25, wherein said predetermined range of expression is below about 1000 copies per cell.
Claim 33
Dependent Claim
47 words
A DNA sequence altered for expression in a host organism other than the one to which it is native, wherein at least three codon pairs of the native sequence have been changed to codon pairs preferred by said host organism in genes expressed at a predetermined level.
Claim 34
Dependent Claim
47 words
A DNA sequence altered for expression in a host organism other than the one to which it is native, wherein at least three codon pairs of the native sequence have been changed to codon pairs preferred by said host organism in genes expressed at a predetermined level.
Claim 35
Dependent Claim
32 words
The sequence of claim 29, wherein said alterations conform the pattern of translational kinetics of said altered sequence in said host organism to that of said native sequence in said native organism.
Claim 36
Dependent Claim
40 words
An organism expressing an exogenous gene native to a different species, wherein said exogenous gene has been tailored for expression in said organism by rational replacement of existing codon pairs with codon pairs producing desired translational kinetics in said organism.
Claim 37
Dependent Claim
40 words
An organism expressing an exogenous gene native to a different species, wherein said exogenous gene has been tailored for expression in said organism by rational replacement of existing codon pairs with codon pairs producing desired translational kinetics in said organism.
Claim 38
Dependent Claim
25 words
The organism of claim 31, wherein said replacement condon pairs are those that, in comparison to random codon pair usage, are under-represented in said organism.
Claim 39
Dependent Claim
25 words
The organism of claim 31, wherein said replacement codon pairs are those that, in comparison to random condon pair usage, are over-represented in said organism.
Claim 40
Independent Claim
40 words
A method for determining the type of organism from which a sample of nucleic acid originated, comprising: determining the nucleotide sequence of said sample; and comparing the codon pairings in said sequence with codon pairing preferences for several possible organisms.
Claim 41
Independent Claim
40 words
A method for determining the type of organism from which a sample of nucleic acid originated, comprising: determining the nucleotide sequence of said sample; and comparing the codon pairings in said sequence with codon pairing preferences for several possible organisms.
Claim 42
Independent Claim
44 words
A method for determining the evolutionary origin of a nucleic acid sample, comprising the steps of: determining the nucleotide sequence of said sample; and comparing the codon pairings in said sequence with codon pairing preferences of genes to which the sample may be related.
Claim 43
Independent Claim
44 words
A method for determining the evolutionary origin of a nucleic acid sample, comprising the steps of: determining the nucleotide sequence of said sample; and comparing the codon pairings in said sequence with codon pairing preferences of genes to which the sample may be related.
Claim 44
Independent Claim
55 words
A method for altering the translational kinetics of only a portion of a gene, comprising the steps of: obtaining, for an organism in which said gene is to be expressed, data regarding the relationship between codon pairing and translational kinetics; and altering at least one codon pairing in said portion in accordance with said data.
Claim 45
Independent Claim
55 words
A method for altering the translational kinetics of only a portion of a gene, comprising the steps of: obtaining, for an organism in which said gene is to be expressed, data regarding the relationship between codon pairing and translational kinetics; and altering at least one codon pairing in said portion in accordance with said data.
Claim 46
Dependent Claim
15 words
The method of claim 36, wherein said alteration introduces a translational pause in said portion.
Claim 47
Dependent Claim
17 words
The method of claim 36, wherein said alteration increases the speed with which said portion is translated.
Claim 48
Independent Claim
119 words
A method for controlling protein folding during expression of an exogenous gene in an engineered organism, comprising the steps of: obtaining data relating to codon pair preferences and relative representation of codon pairs for both a first organism to which said gene is native and a second organism in which said gene is to be expressed; identifying at least one codon pair in said gene that is over- or under-represented to a different extent in said first organism than in said second organism; and altering said identified codon pair to a pair coding for the same amino acid that is represented to generally the same degree in said second organism as the identified pair is in said first organism.
Claim 49
Independent Claim
119 words
A method for controlling protein folding during expression of an exogenous gene in an engineered organism, comprising the steps of: obtaining data relating to codon pair preferences and relative representation of codon pairs for both a first organism to which said gene is native and a second organism in which said gene is to be expressed; identifying at least one codon pair in said gene that is over- or under-represented to a different extent in said first organism than in said second organism; and altering said identified codon pair to a pair coding for the same amino acid that is represented to generally the same degree in said second organism as the identified pair is in said first organism.
Claim 50
Dependent Claim
25 words
The method of claim 39, wherein said identified codon pair is over-represented to a greater degree in said first organism than in said second organism.
Claim 51
Dependent Claim
25 words
The method of claim 39, wherein said identified codon pair is under-represented to a greater degree in said first organism than in said second organism.
Claim 52
Dependent Claim
16 words
The method of claim 39, further comprising the step of expressing said gene in an organism.
Claim 53
Independent Claim
44 words
A method for introducing a translational pause site into a gene to be expressed in a particular organism, comprising the steps of: obtaining, for said organism, information regarding relative representation of codon pairs; and introducing into said desired pause site an over-represented codon pair.
Claim 54
Independent Claim
44 words
A method for introducing a translational pause site into a gene to be expressed in a particular organism, comprising the steps of: obtaining, for said organism, information regarding relative representation of codon pairs; and introducing into said desired pause site an over-represented codon pair.
Claim 55
Dependent Claim
29 words
The method of claim 43, wherein said over-represented codon pair is also at least one standard deviation less abundant than the mean value for codon pairs in said organism.
References Cited (Backward Citations)
US4184917A
Cited
US4468464A
Cited
US4190495A
Cited
US4363877B1
Cited
US4363877A
Cited
US4321365A
Cited
US4356270A
Cited
US4348477A
Cited
US4371625A
Cited
US4332892A
Cited
US4293652A
Cited
US4349629A
Cited
US4262090A
Cited
US4342832A
Cited
US4359535A
Cited
US4399216A
Cited
US4350764A
Cited
US4351901A
Cited
US4396601A
Cited
US4338397A
Cited
US4332898A
Cited
US4394443A
Cited
US4403035A
Cited
USPTO Annuity & Maintenance Windows
| Annuity Stage | Window Opens | Payment Deadline | Surcharge Period Until | Estimated Fee | Status |
|---|---|---|---|---|---|
| 3.5 Years (Year 4) | 1995-01-20 | 1995-07-22 | 1996-01-21 | $2000.00 | Window Closed / Lapsed |
| 7.5 Years (Year 8) | 1999-01-20 | 1999-07-22 | 2000-01-21 | $3760.00 | Window Closed / Lapsed |
| 11.5 Years (Year 12) | 2003-01-20 | 2003-07-22 | 2004-01-21 | $7700.00 | Window Closed / Lapsed |