Gene Patents (Part 2 – the Science, continued)

Part 1 of this series began an exploration of the background of genes and gene patents. We left off noting that one type of synthetic DNA molecule is complementary DNA (cDNA). Because the Federal Circuit in the Myriad case viewed the composition claims of Myriad’s patents as reading on cDNA, an understanding of this chemical molecule is essential for understanding the Court’s holdings in this case.

“In genetics, complementary DNA (cDNA) is DNA synthesized from a messenger RNA (mRNA) template in a reaction catalyzed by the enzyme reverse transcriptase and the enzyme DNA polymerase.[1] cDNA is often used to clone eukaryotic genes in prokaryotes. When scientists want to express a specific protein in a cell that does not normally express that protein (i.e., heterologous expression), they will transfer the cDNA that codes for the protein to the recipient cell.”

According to the central dogma of molecular biology, when synthesizing a protein, a gene’s DNA is transcribed into mRNA which is then translated into protein. One difference between eukaryotic and prokaryotic genes is that eukaryotic genes can contain introns (intervening DNA sequences) which are not coding sequences, in contrast with exons, which are DNA coding sequences. During transcription, all intron RNA is cut from the RNA primary transcript and the remaining pieces of the RNA primary transcript are spliced back together to become mRNA. The mRNA code is then translated into an amino acid chain (sequence) that comprises the newly made protein. Prokaryotic genes have no introns, thus their RNA is not subject to cutting and splicing.

mRNA showing introns and exons

“Often it is desirable to make prokaryotic cells express eukaryotic genes. An approach one might consider is to add eukaryotic DNA directly into a prokaryotic cell, and let it make the protein. However, because eukaryotic DNA has introns, and prokaryotes lack the machinery for removing introns from transcribed RNA, to make this approach work, all intron sequences must be removed from eukaryotic DNA prior to transferring it into the host. This ‘intron-free’ DNA is constructed using ‘intron-free’ mRNA as a template. Thus it is a ‘complementary’ copy of the mRNA, and is thus called complementary DNA (cDNA).”

The word “complementary” is, however, somewhat confusing. In order to understand this meaning, a brief discussion of the structure of ordinary (genome) DNA is essential. In Part 1, it was noted that in the cell, DNA exists as two polynucleotide strands intertwined in a double helix, in which A always pairs with T and G always pairs with C. One of these strands (the coding strand) encodes the protein. The other strand (the non-coding strand) does not. During transcription, mRNA is created from the coding strand, so that the sequence of nucleotides in the mRNA will be the “complement” of those in the coding strand (except that in RNA, uracil (U) pairs with A). When cDNA is created from mRNA, the complementary DNA strand is made. Since the template for the creation of cDNA was already complementary to genome DNA, the “complement of the complement” in the resulting cDNA is the original genome DNA (minus introns, of course). Thus, the cDNA is an accurate reflection of the genetic code in the genomic DNA, and can be used to analyze the genomic DNA.

Another important concept is necessary to understand the various holdings in the Myriad case. This is the chemical structure of DNA.

Part 1 showed the structure of DNA conceptually. However, the actual chemical bonding of the nucleotides in the polynucleotide strand is also important.

“The backbone of the DNA strand is made from alternating phosphate and sugar residues. The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand: the strands are antiparallel. The asymmetric ends of DNA strands are called the 5′ (five prime) and 3′ (three prime) ends, with the 5′ end having a terminal phosphate group and the 3′ end a terminal hydroxyl group. One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the alternative pentose sugar ribose in RNA.”

DNA chemical structure

Thus, genomic DNA is chemically different from cDNA for the following reasons: 1) genomic DNA ordinarily exists in the cell in chromosomes where it is bound to histones; 2) genomic DNA is much longer than cDNA, so that the nucleotide sequence of the cDNA is only a portion of the genomic DNA; and 3) the genomic DNA contains non-coding regions such as introns, while the cDNA contains only exons.

Posted on April 3, 2012, in Patent. Bookmark the permalink. Comments Off on Gene Patents (Part 2 – the Science, continued).

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