Unrestricted Hybridization of Oligonucleotides to Structure-Free DNA

May 3, 2006 - Importantly, while the base analogues enhanced probe−target stability, they did not significantly reduce the specificity of base pairi...
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6978

Biochemistry 2006, 45, 6978-6986

Unrestricted Hybridization of Oligonucleotides to Structure-Free DNA† Howard B. Gamper, Jr.,*,‡ Khalil Arar,§ Alan Gewirtz,| and Ya-Ming Hou‡ Department of Biochemistry and Molecular Biology, Thomas Jefferson UniVersity, Philadelphia, PennsylVania 19107, Sigma-Proligo, 1 Rue Delaunay, Paris 75011, France, and DiVision of Hematology/Oncology, UniVersity of PennsylVania School of Medicine, Philadelphia, PennsylVania 19104 ReceiVed January 8, 2006; ReVised Manuscript ReceiVed March 15, 2006

ABSTRACT: The existence of secondary structure in long single-stranded DNA and RNA is a serious obstacle to the practical use of short oligonucleotide probes (