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We have used DNase I footprinting to examine DNA triple helix formation at a 12 base pair oligopurine.oligopyrimidine sequence, using oligonucleotides that contain combinations of 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine (bis-amino-U, BAU) and 3-methyl-2-aminopyridine (MeP) in place of T and C, respectively. This combination acts cooperatively to enable high affinity triple helix formation at physiological pH. The affinity depends on the number of substitutions and their arrangement; oligonucleotides in which these analogues are evenly distributed throughout the third strand bind much better than those in which they are clustered together.

Original publication

DOI

10.1016/j.febslet.2005.10.056

Type

Journal article

Journal

FEBS Lett

Publication Date

05/12/2005

Volume

579

Pages

6616 - 6620

Keywords

Aminopyridines, Base Sequence, DNA, DNA Footprinting, Deoxyribonuclease I, Hydrogen-Ion Concentration, Nucleic Acid Conformation, Nucleosides, Oligonucleotides, Purines, Uridine