By Donald Zuhn —

Earlier this month, CODA Genomics, Inc. announced that it had been granted U.S. Patent No. 7,262,031.  CODA Genomics, Inc., which derives its name from its Computational Optimized DNA Assembly technology, has exclusively licensed the ‘031 patent from the University of California, Irvine (UCI) Office of Technology Assessment (OTA).  The founders of the Laguna Hills, California-based biotech company, Dr. Richard H. Lathrop (left) and Dr. G. Wesley Hatfield (right), are professors at UCI and named inventors on the ‘031 patent.

According to the statement released by CODA Genomics, the ‘031 patent relates to the use of a global optimization method for the choice of DNA code to make a given protein, wherein properly chosen DNA enables thermodynamically controlled self-assembly of a desired DNA product.  CODA CEO Dr. Robert J Molinari noted that the ‘031 patent provided "broad protection of CODA’s breakthrough technology" which "will allow the company to aggressively market its high-yielding Hot-Rod genes, and other optimized gene variant sets."  According to CODA’s website, the company’s Hot Rod genes are designed to express high levels of protein by removing major pauses in the gene’s open reading frame (ORF) and by improving tRNA codon usage.

The ‘031 patent issued from U.S. Application No. 10/851,383, filed May 21, 2004, and claims the benefit of U.S. Provisional Application No. 60/472,822, filed May 22, 2003.  Independent claims 1 and 42 of the ‘031 patent recites:

1.  A method of synthesizing a DNA sequence encoding a polypeptide, comprising:
    (i) dividing the DNA sequence recursively into small pieces of DNA, wherein adjacent pieces comprise overlapping regions, wherein the division results in at least 3 pieces of DNA;
    (ii) optimizing the sequences of the pieces of DNA resulting from each recursive division in silico by silent codon permutation to strengthen correct hybridizations between adjacent pieces of DNA and to disrupt incorrect hybridizations between all other pieces of DNA resulting from that division;
    (iii) obtaining the optimized small pieces of DNA, wherein the overlapping regions of any adjacent pieces of single-stranded DNA are complementary;
    (iv) combining the pieces of DNA derived from the division of the next-larger piece of DNA;
    (v) allowing the pieces of DNA to self-assemble to form a DNA construct comprising single-stranded DNA segments connected by double-stranded overlap regions;
    (vi) producing the next-larger piece of DNA from the DNA construct; and
    (vii) repeating steps (iv), (v), and (vi) in reverse order of the recursive division in step (i) to produce the DNA sequence.

42.  A method for identifying a set of smaller DNAs suitable for assembly into a larger DNA, where the larger DNA encodes a desired polypeptide, comprising:
    optimizing in silico a set of at least 6 smaller DNAs for assembly together to create the larger DNA, wherein adjacent smaller DNAs comprise overlapping regions, wherein the optimizing comprises permuting silent codons to strengthen correct hybridizations between adjacent pieces of the smaller DNAs and to disrupt all incorrect hybridizations between members of the set, to create a gap between melting temperatures of the lowest melting correct hybridization and the highest melting incorrect hybridization.