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Determining the origin of the stabilization of DNA by 5-aminopropynylation of pyrimidines

Determining the origin of the stabilization of DNA by 5-aminopropynylation of pyrimidines
Determining the origin of the stabilization of DNA by 5-aminopropynylation of pyrimidines
DNA duplexes are stabilized by aminopropynyl modification of pyrimidines at the 5 position. A combination of thermodynamic analyses as a function of ionic strength, NMR, and molecular modeling has been applied to determine the origin of the stabilization. UV melting studies of a dodecamer bearing one, two, or three nonadjacent modified dU and dC and of a single dU(8) in the Dickerson-Drew dodecamer revealed that the modifications are essentially additive in terms of T-m, Delta G, and Delta H, and there is little difference between dU and dC. The free energy change was parsed into electrostatic and nonelectrostatic components, which showed a significant contribution from charge interactions at physiological ionic strength but also a nonelectrostatic contribution that arises in part from hydration. NMR spectroscopy of the modified Dickerson-Drew dodecamer revealed that the conformation of the duplexes is not significantly altered by the modifications, though P-31 NMR shows that the positive charge may affect ionic interactions with the oxygen atoms of the neighboring phosphates. The modified duplex showed significant hydration in both major and minor grooves. The single strands were also analyzed by NMR, which showed evidence of significant stacking interactions in the modified oliconucteotide. Parsing the energy contribution has shown that electrostatics and hydration can produce Substantial increases in thermodynamic stability without significant changes in the conformation of the duplex state. These considerations have significance for the design of oligonucleotides used for hybridization.
triple-helix formation, p-31 chemical-shift, thermodynamic stability, aqueous-solution, hybrid duplexes, nucleic-acids, rna duplex, 3rdstrand, nmr, dodecamer
4710-4719
Booth, James
ce6cfba6-ac11-4b72-afc4-0f15930d0a1a
Brown, Tom
1cd7df32-b945-4ca1-8b59-a51a30191472
Vadhia, Sunil J.
3513cdc0-f25d-4ff1-aaf5-8c1a4ff24ebf
Lack, Oliver
cfbb55aa-1dbb-4088-bb67-0d58f7aa07a0
Cummins, W. Jon
cf061b55-1e7f-4e3a-9ff2-2edb4a2a49c6
Trent, John O.
aabd4141-64bf-4107-9e61-e1407c09d430
Lane, Andrew N.
45ad386f-2308-4610-998b-7913fa4d457c
Booth, James
ce6cfba6-ac11-4b72-afc4-0f15930d0a1a
Brown, Tom
1cd7df32-b945-4ca1-8b59-a51a30191472
Vadhia, Sunil J.
3513cdc0-f25d-4ff1-aaf5-8c1a4ff24ebf
Lack, Oliver
cfbb55aa-1dbb-4088-bb67-0d58f7aa07a0
Cummins, W. Jon
cf061b55-1e7f-4e3a-9ff2-2edb4a2a49c6
Trent, John O.
aabd4141-64bf-4107-9e61-e1407c09d430
Lane, Andrew N.
45ad386f-2308-4610-998b-7913fa4d457c

Booth, James, Brown, Tom, Vadhia, Sunil J., Lack, Oliver, Cummins, W. Jon, Trent, John O. and Lane, Andrew N. (2005) Determining the origin of the stabilization of DNA by 5-aminopropynylation of pyrimidines. Biochemistry, 44 (12), 4710-4719. (doi:10.1021/bi047561d).

Record type: Article

Abstract

DNA duplexes are stabilized by aminopropynyl modification of pyrimidines at the 5 position. A combination of thermodynamic analyses as a function of ionic strength, NMR, and molecular modeling has been applied to determine the origin of the stabilization. UV melting studies of a dodecamer bearing one, two, or three nonadjacent modified dU and dC and of a single dU(8) in the Dickerson-Drew dodecamer revealed that the modifications are essentially additive in terms of T-m, Delta G, and Delta H, and there is little difference between dU and dC. The free energy change was parsed into electrostatic and nonelectrostatic components, which showed a significant contribution from charge interactions at physiological ionic strength but also a nonelectrostatic contribution that arises in part from hydration. NMR spectroscopy of the modified Dickerson-Drew dodecamer revealed that the conformation of the duplexes is not significantly altered by the modifications, though P-31 NMR shows that the positive charge may affect ionic interactions with the oxygen atoms of the neighboring phosphates. The modified duplex showed significant hydration in both major and minor grooves. The single strands were also analyzed by NMR, which showed evidence of significant stacking interactions in the modified oliconucteotide. Parsing the energy contribution has shown that electrostatics and hydration can produce Substantial increases in thermodynamic stability without significant changes in the conformation of the duplex state. These considerations have significance for the design of oligonucleotides used for hybridization.

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More information

Published date: 29 March 2005
Keywords: triple-helix formation, p-31 chemical-shift, thermodynamic stability, aqueous-solution, hybrid duplexes, nucleic-acids, rna duplex, 3rdstrand, nmr, dodecamer

Identifiers

Local EPrints ID: 20729
URI: https://eprints.soton.ac.uk/id/eprint/20729
PURE UUID: da83d59a-b2bf-4b31-9acd-e322fa7cc659

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Date deposited: 01 Mar 2006
Last modified: 17 Jul 2017 16:28

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Contributors

Author: James Booth
Author: Tom Brown
Author: Sunil J. Vadhia
Author: Oliver Lack
Author: W. Jon Cummins
Author: John O. Trent
Author: Andrew N. Lane

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