The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization.

TitleThe illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization.
Publication TypeJournal Article
Year of Publication2013
AuthorsGarhyan J, Gharaibeh RZ, McGee S, Gibas CJ
JournalBMC Res Notes
Date Published2013 Feb 27
KeywordsBase Sequence, Chromatography, High Pressure Liquid, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Oligonucleotides, Solutions, Surface Properties

<p><b>BACKGROUND: </b>Hybridization based assays and capture systems depend on the specificity of hybridization between a probe and its intended target. A common guideline in the construction of DNA microarrays, for instance, is that avoiding complementary stretches of more than 15 nucleic acids in a 50 or 60-mer probe will eliminate sequence specific cross-hybridization reactions. Here we present a study of the behavior of partially matched oligonucleotide pairs with complementary stretches starting well below this threshold complementarity length - in silico, in solution, and at the microarray surface. The modeled behavior of pairs of oligonucleotide probes and their targets suggests that even a complementary stretch of sequence 12 nt in length would give rise to specific cross-hybridization. We designed a set of binding partners to a 50-mer oligonucleotide containing complementary stretches from 6 nt to 21 nt in length.</p><p><b>RESULTS: </b>Solution melting experiments demonstrate that stable partial duplexes can form when only 12 bp of complementary sequence are present; surface hybridization experiments confirm that a signal close in magnitude to full-strength signal can be obtained from hybridization of a 12 bp duplex within a 50mer oligonucleotide.</p><p><b>CONCLUSIONS: </b>Microarray and other molecular capture strategies that rely on a 15 nt lower complementarity bound for eliminating specific cross-hybridization may not be sufficiently conservative.</p>

Alternate JournalBMC Res Notes
PubMed ID23445545
PubMed Central IDPMC3599332
Grant ListR01-GM072619-01 / GM / NIGMS NIH HHS / United States