Oligonucleotides as recognition and catalytic elements

Abstract

Oligonucleotides function as recognition elements for both nucleic acids and proteins in many ways, starting from their basic function as genetic material recognizing the complementary sequences of RNA or DNA, through their role as genetic regulatory elements in the form of antisense DNA/RNA, interfering RNA (RNAi) as well as enzymatic activities such as trans-cleaving ribozymes. Oligonucleotides can also serve as recognition elements for proteins in the form of aptamers. All of these functions are derived from the basic primary, secondary, and tertiary structures along with their combinatorial nature, which allows vast variability within even short sequences. For biotechnology, the utility of oligonucleotides goes far beyond their basic function as a carrier of genetic information. Oligonucleotides are widely used as recognition elements for a large number of DNA and protein manipulation technologies, including numerous methods for DNA amplification, manipulation (e.g., mutation insertion or repair), and DNA sequence recognition and analysis. They are used for manipulation of gene expression including the use of ribozymes to catalyze RNA digestion, and siRNA and anti-sense RNA/DNA used for gene silencing in both in vitro and in vivo. In addition, they serve as an alternative to antibodies as ligands for protein detection. The term oligonucleotide (or oligo) refers to a short segment of DNA or RNA commonly synthesized today by polymerizing nucleotide precursors using automated synthesizers. Although most oligos used in molecular biology are short in the range of 20-30 bases (or mer), the term is used here also to refer to longer sequences (e.g., ~200 bases) and to ribozymes, which are traditionally not viewed as oligos. In this manuscript, we describe the basic structure of oligonucleotides relevant to general utility in molecular biology and biotechnology. This utility includes function as recognition elements, basic utility for DNA amplification, recognition and manipulation, application for the regulation of gene expression and function and utility as protein recognition elements. © Springer Science+Business Media, LLC 2010.