Genomic Versus cDNA Clones

A gene can take varying forms, and so can gene clones. The protein-coding regions of most eukaryotic genes are interrupted by noncoding sequences called introns, which are ultimately excluded from the mature messenger RNA (mRNA) after the gene is transcribed. In addition to the protein-coding sequences, all genes contain "upstream" and "downstream" regulatory sequences that control when, in which tissues, and under what circumstances the gene is transcribed. A clone containing the entire region of a gene as it exists on the chromosome, including introns and nontran-scribed regulatory sequences, is called a genomic clone because it is derived directly from genomic, or chromosomal, DNA.

It is also possible to clone a gene directly from its messenger RNA transcript, from which all introns have been removed. This type of clone, called a complementary DNA or cDNA clone, includes only the protein-coding sequences and upstream and downstream sequences that do not code for amino acids but that may control how the mRNA transcript gets translated to protein.

To prepare cDNA a researcher starts with mRNA and then makes a complementary single-stranded DNA copy using the enzyme reverse transcriptase. Reverse transcriptase is a DNA polymerase that synthesizes DNA based on an RNA template that is produced by retroviruses. After the mRNA strand is digested away by another enzyme, called RNase H, DNA poly-merase can synthesize a second DNA strand by using the newly made first strand cDNA as a template.

Because cDNAs lack introns, the protein-coding region in a cDNA molecule is contained in a single uninterrupted sequence, called an open reading frame, or ORF. This makes cDNA clones extremely useful for predicting the amino acid sequence of the protein that a gene encodes. It also makes it possible to direct protein synthesis from a eukaryotic cDNA clone in a bacterium, which cannot splice introns. With introns still present in a cloned gene, the bacteria will misinterpret the intron sequences as protein-encoding sequences. The resulting incorrect messanger RNA will encode a protein with an incorrect amino acid.

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