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DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine

DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine
DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine
We have prepared triplex-forming oligonucleotides containing the nucleotide analogue 5-dimethylaminopropargyl deoxyuridine (DMAPdU) in place of thymidine and examined their ability to form intermolecular triple helices by thermal melting and DNase I footprinting studies. The results were compared with those for oligonucleotides containing 5-aminopropargyl-dU (APdU), 5-guanidinopropargyl-dU (GPdU) and 5-propynyl dU (PdU). We find that DMAPdU enhances triplex stability relative to T, though slightly less than the other analogues that bear positive charges (T << PdU < DMAPdU < APdU < GPdU). For oligonucleotides that contain multiple substitutions with DMAPdU dispersed residues are more effective than clustered combinations. DMAPdU will be especially useful as a nucleotide analogue as, unlike APdU and GPdU, the base does not require protection during oligonucleotide synthesis and it can therefore be used with other derivatives that require mild deprotection conditions.
0305-1048
1288-1296
Rusling, David A.
d08f1f97-f8a9-4980-a025-ae41c23a938f
Peng, Guomei
5ed31240-5067-4da5-9e84-aaab79fa33cd
Srinivasan, Natarajan
d853c4c5-da37-4a46-b102-9bb285812d32
Fox, Keith R
9da5debc-4e45-473e-ab8c-550d1104659f
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Rusling, David A.
d08f1f97-f8a9-4980-a025-ae41c23a938f
Peng, Guomei
5ed31240-5067-4da5-9e84-aaab79fa33cd
Srinivasan, Natarajan
d853c4c5-da37-4a46-b102-9bb285812d32
Fox, Keith R
9da5debc-4e45-473e-ab8c-550d1104659f
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89

Rusling, David A., Peng, Guomei, Srinivasan, Natarajan, Fox, Keith R and Brown, Tom (2009) DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine. Nucleic Acids Research, 37 (4), 1288-1296. (doi:10.1093/nar/gkn1060).

Record type: Article

Abstract

We have prepared triplex-forming oligonucleotides containing the nucleotide analogue 5-dimethylaminopropargyl deoxyuridine (DMAPdU) in place of thymidine and examined their ability to form intermolecular triple helices by thermal melting and DNase I footprinting studies. The results were compared with those for oligonucleotides containing 5-aminopropargyl-dU (APdU), 5-guanidinopropargyl-dU (GPdU) and 5-propynyl dU (PdU). We find that DMAPdU enhances triplex stability relative to T, though slightly less than the other analogues that bear positive charges (T << PdU < DMAPdU < APdU < GPdU). For oligonucleotides that contain multiple substitutions with DMAPdU dispersed residues are more effective than clustered combinations. DMAPdU will be especially useful as a nucleotide analogue as, unlike APdU and GPdU, the base does not require protection during oligonucleotide synthesis and it can therefore be used with other derivatives that require mild deprotection conditions.

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More information

Published date: 9 March 2009
Organisations: Biological Sciences

Identifiers

Local EPrints ID: 142597
URI: http://eprints.soton.ac.uk/id/eprint/142597
ISSN: 0305-1048
PURE UUID: 2157756d-daa9-4455-84a7-09d5cda09fbc
ORCID for David A. Rusling: ORCID iD orcid.org/0000-0002-7442-686X
ORCID for Keith R Fox: ORCID iD orcid.org/0000-0002-2925-7315

Catalogue record

Date deposited: 01 Apr 2010 15:35
Last modified: 14 Mar 2024 02:33

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Contributors

Author: David A. Rusling ORCID iD
Author: Guomei Peng
Author: Natarajan Srinivasan
Author: Keith R Fox ORCID iD
Author: Tom Brown

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