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Fluorescent properties of DNA base analogue tC upon incorporation into DNA - negligible influence of neighbouring bases on fluorescence quantum yield

Fluorescent properties of DNA base analogue tC upon incorporation into DNA - negligible influence of neighbouring bases on fluorescence quantum yield
Fluorescent properties of DNA base analogue tC upon incorporation into DNA - negligible influence of neighbouring bases on fluorescence quantum yield
The quantum yield of the fluorescent tricyclic cytosine analogue, 1,3-diaza-2-oxophenothiazine, tC, is high and virtually unaffected by incorporation into both single- and double-stranded DNA irrespective of neighbouring bases (0.17-0.24 and 0.16-0.21, respectively) and the corresponding fluorescence decay curves are all mono-exponential, properties that are unmatched by any base analogue so far. The fluorescence lifetimes increase when going from tC free in solution (3.2 ns) to single- and double-stranded DNA (on average 5.7 and 6.3 ns, respectively). The mono-exponential decays further support previous NMR results where it was found that tC has a well-defined position and geometry within the DNA helix. Furthermore, we find that the oxidation potential of tC is 0.4 V lower than for deoxyguanosine, the natural base with the lowest oxidation potential. This suggests that tC may be of interest in charge transfer studies in DNA as an electron hole acceptor. We also present a novel synthetic route to the phosphoramidite form of tC. The results presented here together with previous work show that tC is a very good C-analogue that induces minimal perturbation to the native structure of DNA. This makes tC unique as a fluorescent base analogue and is thus highly interesting in a range of applications for studying e.g. structure, dynamics and kinetics in nucleic acid systems.
pteridine nucleoside analogs, mediated electron-transfer, nucleic-acids, guanosine analog, 2-aminopurine, oligonucleotides, dynamics, derivatives, stacking, cytosine
0305-1048
5019-5025
Sandin, Peter
f7324993-b21e-4575-ae67-fd3223624030
Wilhelmsson, Marcus
59294366-b005-4691-a167-1d628ecda968
Lincoln, Per
f1edcf40-411d-4f54-bd94-d13394c011d4
Powers, Vicki E.C.
0646d625-5039-454c-a8ad-0da6bc72ae8a
Brown, Tom
1cd7df32-b945-4ca1-8b59-a51a30191472
Albinsson, Bo
1571067f-df46-43f7-96b9-52dc43278777
Sandin, Peter
f7324993-b21e-4575-ae67-fd3223624030
Wilhelmsson, Marcus
59294366-b005-4691-a167-1d628ecda968
Lincoln, Per
f1edcf40-411d-4f54-bd94-d13394c011d4
Powers, Vicki E.C.
0646d625-5039-454c-a8ad-0da6bc72ae8a
Brown, Tom
1cd7df32-b945-4ca1-8b59-a51a30191472
Albinsson, Bo
1571067f-df46-43f7-96b9-52dc43278777

Sandin, Peter, Wilhelmsson, Marcus, Lincoln, Per, Powers, Vicki E.C., Brown, Tom and Albinsson, Bo (2005) Fluorescent properties of DNA base analogue tC upon incorporation into DNA - negligible influence of neighbouring bases on fluorescence quantum yield. Nucleic Acids Research, 33 (16), 5019-5025. (doi:10.1093/nar/gki790).

Record type: Article

Abstract

The quantum yield of the fluorescent tricyclic cytosine analogue, 1,3-diaza-2-oxophenothiazine, tC, is high and virtually unaffected by incorporation into both single- and double-stranded DNA irrespective of neighbouring bases (0.17-0.24 and 0.16-0.21, respectively) and the corresponding fluorescence decay curves are all mono-exponential, properties that are unmatched by any base analogue so far. The fluorescence lifetimes increase when going from tC free in solution (3.2 ns) to single- and double-stranded DNA (on average 5.7 and 6.3 ns, respectively). The mono-exponential decays further support previous NMR results where it was found that tC has a well-defined position and geometry within the DNA helix. Furthermore, we find that the oxidation potential of tC is 0.4 V lower than for deoxyguanosine, the natural base with the lowest oxidation potential. This suggests that tC may be of interest in charge transfer studies in DNA as an electron hole acceptor. We also present a novel synthetic route to the phosphoramidite form of tC. The results presented here together with previous work show that tC is a very good C-analogue that induces minimal perturbation to the native structure of DNA. This makes tC unique as a fluorescent base analogue and is thus highly interesting in a range of applications for studying e.g. structure, dynamics and kinetics in nucleic acid systems.

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More information

Published date: 2005
Keywords: pteridine nucleoside analogs, mediated electron-transfer, nucleic-acids, guanosine analog, 2-aminopurine, oligonucleotides, dynamics, derivatives, stacking, cytosine

Identifiers

Local EPrints ID: 20906
URI: http://eprints.soton.ac.uk/id/eprint/20906
ISSN: 0305-1048
PURE UUID: 6c743f03-ae67-403d-a0d7-d0b38c94ac0f

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Date deposited: 01 Mar 2006
Last modified: 15 Jul 2019 19:25

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Contributors

Author: Peter Sandin
Author: Marcus Wilhelmsson
Author: Per Lincoln
Author: Vicki E.C. Powers
Author: Tom Brown
Author: Bo Albinsson

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