Synthetic nucleic acids from aquatic species

A polynucleotide which hybridizes under at least low stringency hybridization conditions to the synthetic nucleic acid molecule comprising SEQ ID NO:

• 1 (hGreen II), nucleotides 22 to 702 of SEQ ID NO:3 (2M1-h), nucleotides 22 to 702 of SEQ ID NO:5 (2M1-h1), nucleotides 22 to 702 of SEQ ID NO:7 (2M1-h2), nucleotides 22 to 702 of SEQ ID NO:9 (2M1-h3), nucleotides 22 to 702 of SEQ ID NO:11 (2M1-h4), nucleotides 22 to 702 of SEQ ID NO:13 (2M1-h5), nucleotides 39 to 719 of SEQ ID NO:15 (2M1-h6), or nucleotides 38 to 718 of SEQ ID NO:
• 17 (2M 1-h7), or the complement thereof.

A method to prepare a synthetic nucleic acid molecule comprising an open reading frame, comprising:

• a) altering a plurality of transcription regulatory sequences in a parent nucleic acid sequence which encodes a fluorescent polypeptide to yield a synthetic nucleic acid molecule which has at least 3-fold fewer transcription regulatory sequences relative to the parent nucleic acid sequence;
• and
• b) altering greater than 25% of the codons in the synthetic nucleic acid sequence which has a decreased number of transcription regulatory sequences to yield a further synthetic nucleic acid molecule, wherein the codons which are altered do not result in an increased number of transcription regulatory sequences, wherein the further synthetic nucleic acid molecule encodes a polypeptide with at least 85% amino acid sequence identity to the polypeptide encoded by the parent nucleic acid sequence.

A method to prepare a synthetic nucleic acid molecule comprising an open reading frame, comprising:

• a) altering greater than 25% of the codons in a parent nucleic acid sequence which encodes a fluorescent polypeptide to yield a codon-altered synthetic nucleic acid molecule, and
• b) altering a plurality of transcription regulatory sequences in the codon-altered synthetic nucleic acid molecule to yield a further synthetic nucleic acid molecule which has at least 3-fold fewer transcription regulatory sequences relative to a synthetic nucleic acid molecule with codons which differ from the corresponding codons in the parent nucleic acid sequence, and wherein the further synthetic nucleic acid molecule encodes a polypeptide with at least 85% amino acid sequence identity to the fluorescent polypeptide encoded by the parent nucleic acid sequence.

A method for preparing at least two synthetic nucleic acid molecules which are codon distinct versions of a parent nucleic acid sequence which encodes a fluorescent polypeptide, comprising:

• a) altering a parent nucleic acid sequence to yield a synthetic nucleic acid molecule having an increased number of a first plurality of codons that are employed more frequently in a selected host cell relative to the number of those codons in the parent nucleic acid sequence;
• and
• b) altering the parent nucleic acid sequence to yield a further synthetic nucleic acid molecule having an increased number of a second plurality of codons that are employed more frequently in the host cell relative to the number of those codons in the parent nucleic acid sequence, wherein the first plurality of codons is different than the second plurality of codons, and wherein the synthetic and the further synthetic nucleic acid molecules encode the same polypeptide.