Codon pair utilization

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.

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.

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.

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.

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.

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.

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.

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.