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Secondary binding sites for heavily modified triplex forming oligonucleotides.

ABSTRACT: 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.

SUBMITTER: Cardew AS

PROVIDER: S-EPMC3333850 | biostudies-other | 2012 Apr

REPOSITORIES: biostudies-other

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Secondary binding sites for heavily modified triplex forming oligonucleotides.

Cardew Antonia S AS Brown Tom T Fox Keith R KR

Nucleic acids research 20111217 8

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 se ...[more]

PMID: 22180535

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