title: The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, USA.
authors: Jaishree
authors: J
authors: Garhyan
authors: Raad Z
authors: RZ
authors: Gharaibeh
authors: Stephen
authors: S
authors: McGee
authors: Cynthia J
authors: CJ
authors: Gibas
mesh_terms: D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000737:chemistry*; D012996:Solutions; D013499:Surface Properties
chemical_list: D009841:Oligonucleotides; D012996:Solutions