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In order to enhance DNA triple helix stability synthetic oligonucleotides have been developed that bear amino groups on the sugar or base. One of the most effective of these is bis-amino-U (B), which possesses 5-propargylamino and 2'-aminoethoxy modifications. Inclusion of this modified nucleotide not only greatly enhances triplex stability, but also increases the affinity for related sequences. We have used a restriction enzyme protection, selection and amplification assay (REPSA) to isolate sequences that are bound by the heavily modified 9-mer triplex-forming oligonucleotide B(6)CBT. The isolated sequences contain A(n) tracts (n = 6), suggesting that the 5'-end of this TFO was responsible for successful triplex formation. DNase I footprinting with these sequences confirmed triple helix formation at these secondary targets and demonstrated no interaction with similar oligonucleotides containing T or 5-propargylamino-dU.

Original publication

DOI

10.1093/nar/gkr1119

Type

Journal article

Journal

Nucleic Acids Res

Publication Date

04/2012

Volume

40

Pages

3753 - 3762

Keywords

Base Sequence, Binding Sites, DNA, DNA Footprinting, Deoxyribonuclease I, Deoxyribonucleases, Type II Site-Specific, Deoxyuridine, Oligonucleotides, Uridine