Excitation energy transfer in DNA: Duplex melting and transfer from normal bases to 2-aminopurine

Nordlund, Thomas M.; Xu, Daguang; Evans, Kervin O.

doi:10.1021/bi00096a020

Cited by 84 publications

(101 citation statements)

References 26 publications

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“…One of them consists in observing photosensitized fluorescence from an energy acceptor (intercalator or modified base). [14][15][16][17][18] The problem is that such investigations provide information about excitation transfer between DNA bases and the energy acceptor, and the conclusions cannot necessarily be extrapolated to energy transfer occurring among natural bases. According to another approach, fluorescence of double helices containing only natural bases is observed.…”

Section: Old Questions Recent Approachesmentioning

confidence: 99%

Excited states and energy transfer among DNA bases in double helices

Markovitsi

Gustavsson

Talbot

2007

Photochem Photobiol Sci

108

174

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Abstract:The study of excited states and energy transfer in DNA double helices has recently gained new interest connected to the development of computational techniques and that of femtosecond spectroscopy. The present article points out contentious questions regarding the nature of the excited states and the occurrence of energy transfer and shows how they are currently approached. Using as example the polymer poly(dA).poly(dT), composed of about 2000 adenine-thymine pairs, a model is proposed on the basis of time-resolved measurements (fluorescence decays, fluorescence anisotropy decays and fluorescence spectra, obtained with femtosecond resolution), associated to steady-state spectra. According to this qualitative model, excitation at 267 nm populates excited states that are delocalized over a few bases (excitons). Ultrafast internal conversion directs the excited state population to the lower part of the exciton band giving rise to fluorescence. Questions needing further investigations, both theoretical and experimental, are underlined with particular emphasis on delicate points related to the complexity and the plasticity of these systems.

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Section: Old Questions Recent Approachesmentioning

confidence: 99%

Excited states and energy transfer among DNA bases in double helices

Markovitsi

Gustavsson

Talbot

2007

Photochem Photobiol Sci

108

174

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“…For performing (time-resolved) fluorescence spectroscopy, the use of extrinsic probes is a prerequisite because of the very low fluorescence quantum yield of the natural nucleic acids [5]. The adenine analogue 2-aminopurine (2AP) is a widely used probe for these purposes [6][7][8][9], because of its high fluorescence quantum yield (0.66), its redshifted absorption allowing selective excitation, and its property to build into the DNA B-helix without significant structural disturbance [10,11]. Introduction of 2AP into DNA causes a large reduction of the fluorescence quantum yield, which is attributed to stacking interactions with the neighboring bases possibly causing charge transfer processes [8].…”

Section: Introductionmentioning

confidence: 99%

Electronic states in 2-aminopurine revealed by ultrafast transient absorption and target analysis

Larsen

Stokkum

Groot

et al. 2003

Chemical Physics Letters

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Subpicosecond polarized transient-absorption measurements on the fluorescent adenine analogue 2-aminopurine have been performed in the wavelength region from 320 to 690 nm. Global target analysis of the data reveals structural heterogeneity of the chromophore in the excited state. Two distinct states with remarkably different spectroscopic properties were resolved. One state does show stimulated emission, whereas the other state does not and exposes a very long excited-state lifetime.

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“…he nucleotide 2-aminopurine (2AP) has been used as a site-specific probe of nucleic acid structure and dynamics (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11) because it base pairs with cytosine in a wobble configuration (4,5,12) or with thymine in a Watson-Crick geometry (7,11). Thermodynamic measurements of DNAs containing 2AP:C or 2AP:T show that the former pairing is more destabilizing (11,12).…”

mentioning

confidence: 99%

2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking

Jean

Hall

2000

Proc. Natl. Acad. Sci. U.S.A.

334

208

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2-Aminopurine (2AP) is a fluorescent analog of guanosine and adenosine and has been used to probe nucleic acid structure and dynamics. Its spectral features in nucleic acids have been interpreted phenomenologically, in the absence of a rigorous electronic description of the context-dependence of 2AP fluorescence. Now, by using time-dependent density functional theory, we describe the excited-state properties of 2AP in a B-form dinucleotide stacked with guanosine, adenosine, cytosine, or thymine. Calculations predict that 2AP fluorescence is quenched statically when stacked with purines, because of mixing of the molecular orbitals in the ground state. In contrast, quenching is predicted to be dynamic when 2AP is stacked with pyrimidines, because of formation of a low-lying dark excited state. The different quenching mechanisms will result in different experimentally measured fluorescence lifetimes and quantum yields. The nucleotide 2-aminopurine (2AP) has been used as a site-specific probe of nucleic acid structure and dynamics (1-11) because it base pairs with cytosine in a wobble configuration (4,5,12) or with thymine in a Watson-Crick geometry (7,11). Thermodynamic measurements of DNAs containing 2AP:C or 2AP:T show that the former pairing is more destabilizing (11,12). Incorporating 2AP into DNA quenches its fluorescence (2, 8, 11), reducing its quantum yield from that of the free nucleoside (0.65 in aqueous solution). This reduction is attributed to stacking interactions with nearest neighbor nucleobases, and, therefore, fluorescence properties of 2AP have been used to probe the equilibrium stacking properties of DNA duplexes containing these mismatched pairs (2,8,10). Although the fluorescence decay of 2AP in solution is single exponential, with a lifetime of Ϸ10 ns, in the context of a DNA molecule, four decay components, from 50 ps to 8 ns, are typically needed to describe its lifetime (2). The short decay time observed for 2AP in a duplex is attributed to the fully stacked state, whereas the longest lifetime comes from unstacked 2AP (2, 7). The distribution of stacked states can be altered by temperature, solvent, flanking bases, and bound protein, and so all of these conditions can be probed by using 2AP fluorescence. Dynamics of stacked bases adjacent to a mutagenic mismatch in DNA (such as 2AP:C and 2AP:T) may be part of the recognition mechanism by replication͞repair enzymes (3, 13), so interpretation of 2AP fluorescence data is critical for describing these environments.To understand the effect of base stacking on fluorescent properties of 2AP, we have used time-dependent density functional theory (TDDFT) (14, 15) to calculate the excited-state properties of 2AP alone and in stacked B-and A-form dinucleotides (dimers). Analysis of monomer calculations indicates the accuracy with which TDDFT describes spectral properties: excited-state transition energies, transition dipole directions, and oscillator strengths for 2AP, thymine, cytosine, adenine, and guanine (see figures) are in excellent agreement w...

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Excitation energy transfer in DNA: Duplex melting and transfer from normal bases to 2-aminopurine

Cited by 84 publications

References 26 publications

Excited states and energy transfer among DNA bases in double helices

Excited states and energy transfer among DNA bases in double helices

Electronic states in 2-aminopurine revealed by ultrafast transient absorption and target analysis

2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking

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