Hybridization methods are based on the ability of two nucleic acid strands that have complementary base sequences (i.e„ are homologous) to specifically bond with each other and form a double-stranded molecule, or duplex or hybrid. This duplex formation is driven by the consistent manner in which the base adenine always bonds to thymine, while the bases guanine and cytosine always form a bonding pair (see Figure 2-2). Because hybridization requires nucleic acid sequence homology, a positive hybridization reaction between two nucleic acid strands, each from a different source, indicates genetic relatedness between the two organisms that donated each of the nucleic acid strands for the hybridization reaction.
Hybridization assays require that one nucleic acid strand (the probe) originate from an organism of known identity and the other strand (the target) originate from an unknown organism to be detected or identified (Figure 8-1). Positive hybridization identifies the unknown organism as being the same as the probe-source organism. With a négative hybridization test the organism remains undetected or unidentified. The single-stranded nucleic acid components used in hybridization may be either RNA or DNA so that DNA-DNA, DNA-RNA, and even RNA-RNA duplexes may form.
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