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Stable DNA triple helix formation using oligonucleotides containing 2'-aminoethoxy,5-propargylamino-U

Stable DNA triple helix formation using oligonucleotides containing 2'-aminoethoxy,5-propargylamino-U
Stable DNA triple helix formation using oligonucleotides containing 2'-aminoethoxy,5-propargylamino-U
We have prepared oligonucleotides containing the novel base analogue 2'-aminoethoxy,5-proparaylamino-U in place of thymidine and examined their ability to form intermolecular and intramolecular triple helices by DNase I footprinting and thermal melting studies. The results were compared with those for oligonucleotides containing 5-propargylamino-dU and 2'-aminoethoxy-T. We find that the bis-substituted derivative produces a large increase in triplex stability, much greater than that produced by either of the monosubstituted analogues, which are roughly equipotent with each other. Intermolecular triplexes with 9-mer oligonucleotides containing three or four base modifications generate footprints at submicromolar concentrations even at pH 7.5, in contrast to the unmodified oligonucleotide, which failed to produce a footprint at pH 5.0, even at 30 muM. UV- and fluorescence melting studies with intramolecular triplexes confirmed that the bis-modified base produces a much greater increase in T-m than either modification alone.
acridine-containing oligonucleotides, targeted gene knockout, double-stranded dna, forming oligonucleotides, 2', -aminoethoxy-modifiedoligonucleotides, dual recognition, stability, duplex, sites, 5-(1-propynyl)-2', -deoxyuridine
0006-2960
7224-7231
Sollogoub, Matthieu
e9a6b887-5184-49d6-93bf-5a3baf392e2b
Darby, Richard A.J.
7f45c51f-720f-48f6-ba71-647b6460da8d
Cuenoud, Bernard
fa0f8df8-b97a-4303-966c-74d5f5803d8d
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Fox, Keith R.
9da5debc-4e45-473e-ab8c-550d1104659f
Sollogoub, Matthieu
e9a6b887-5184-49d6-93bf-5a3baf392e2b
Darby, Richard A.J.
7f45c51f-720f-48f6-ba71-647b6460da8d
Cuenoud, Bernard
fa0f8df8-b97a-4303-966c-74d5f5803d8d
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Fox, Keith R.
9da5debc-4e45-473e-ab8c-550d1104659f

Sollogoub, Matthieu, Darby, Richard A.J., Cuenoud, Bernard, Brown, Tom and Fox, Keith R. (2002) Stable DNA triple helix formation using oligonucleotides containing 2'-aminoethoxy,5-propargylamino-U. Biochemistry, 41 (23), 7224-7231. (doi:10.1021/bi020164n).

Record type: Article

Abstract

We have prepared oligonucleotides containing the novel base analogue 2'-aminoethoxy,5-proparaylamino-U in place of thymidine and examined their ability to form intermolecular and intramolecular triple helices by DNase I footprinting and thermal melting studies. The results were compared with those for oligonucleotides containing 5-propargylamino-dU and 2'-aminoethoxy-T. We find that the bis-substituted derivative produces a large increase in triplex stability, much greater than that produced by either of the monosubstituted analogues, which are roughly equipotent with each other. Intermolecular triplexes with 9-mer oligonucleotides containing three or four base modifications generate footprints at submicromolar concentrations even at pH 7.5, in contrast to the unmodified oligonucleotide, which failed to produce a footprint at pH 5.0, even at 30 muM. UV- and fluorescence melting studies with intramolecular triplexes confirmed that the bis-modified base produces a much greater increase in T-m than either modification alone.

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More information

Published date: 11 June 2002
Keywords: acridine-containing oligonucleotides, targeted gene knockout, double-stranded dna, forming oligonucleotides, 2', -aminoethoxy-modifiedoligonucleotides, dual recognition, stability, duplex, sites, 5-(1-propynyl)-2', -deoxyuridine

Identifiers

Local EPrints ID: 19859
URI: http://eprints.soton.ac.uk/id/eprint/19859
ISSN: 0006-2960
PURE UUID: 44964ba3-94c0-48a3-a664-68a094b6a046
ORCID for Keith R. Fox: ORCID iD orcid.org/0000-0002-2925-7315

Catalogue record

Date deposited: 22 Feb 2006
Last modified: 09 Jan 2022 02:35

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Contributors

Author: Matthieu Sollogoub
Author: Richard A.J. Darby
Author: Bernard Cuenoud
Author: Tom Brown
Author: Keith R. Fox ORCID iD

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