Codon pair utilization
First Claim
1. 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.
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Accused Products
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.
156 Citations
44 Claims
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1. A method for determining relative native codon pairing preferences in an organism, comprising the steps of:
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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. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22)
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11. 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:
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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. - View Dependent Claims (12, 13, 14, 15, 16)
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17. A method for altering a gene of a first organism for expression in a second organism, comprising the steps of:
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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. - View Dependent Claims (18, 19, 20, 23, 24)
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25. 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. - View Dependent Claims (26, 27, 28)
- 29. 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.
- 31. 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.
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34. A method for determining the type of organism from which a sample of nucleic acid originated, comprising:
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determining the nucleotide sequence of said sample; and comparing the codon pairings in said sequence with codon pairing preferences for several possible organisms.
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35. A method for determining the evolutionary origin of a nucleic acid sample, comprising the steps of:
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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.
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36. A method for altering the translational kinetics of only a portion of a gene, comprising the steps of:
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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. - View Dependent Claims (37, 38)
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39. A method for controlling protein folding during expression of an exogenous gene in an engineered organism, comprising the steps of:
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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. - View Dependent Claims (40, 41, 42)
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43. A method for introducing a translational pause site into a gene to be expressed in a particular organism, comprising the steps of:
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obtaining, for said organism, information regarding relative representation of codon pairs; and introducing into said desired pause site an over-represented codon pair. - View Dependent Claims (44)
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Specification