Ultrafast Excited-State Dynamics in Nucleic Acids

Crespo‐Hernández, Carlos E.; Cohen, Boiko; Hare, Patrick M.; Kohler, Bern

doi:10.1021/cr0206770

Cited by 1,214 publications

(1,740 citation statements)

References 343 publications

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“…1,23,26,27 We obtain a quantum yield for the G9 quadruplex of 2.4 3 10 24 , which is between the values for GpG and poly(G). The quantum yield is not a simple linear function of the number of guanines in the sequence, which we attribute to structural differences.…”

Section: Discussionmentioning

confidence: 63%

“…The quantum yield is not a simple linear function of the number of guanines in the sequence, which we attribute to structural differences. 23,24,26,27 GMP is monomeric in solution, whereas G9 and poly(G) adopt tetrastranded structures. 35 Quadruplex formation has been hypothesized to affect excited-state lifetimes on the basis of work with a polyG sequence containing 20 guanines 27 which is similar to a sequence containing 20 contiguous Gs flanked by thymine residues forms a quadruplex in sodium-containing buffer.…”

Section: Discussionmentioning

confidence: 99%

“…21 Upper limits for the lowest excited singlet lifetimes are 1 ps for the mononucleotides cytosine and thymine and 10 ps for adenine and guanine. 23 Some DNA polymers have been reported to have excited-state lifetimes of 100 ps and even upto 1 ns. 14,24,25 The quantum yield of polyG at room temperature in aqueous solution, however, is 4.7 3 10 24 , which makes it the native DNA sequence with the highest intrinsic fluorescence.…”

Section: Introductionmentioning

confidence: 99%

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Fluorescence of unmodified oligonucleotides: A tool to probe G‐quadruplex DNA structure

Méndez

Szalai

2009

Biopolymers

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Fluorescence of unmodified oligonucleotides has not been exploited for guanine‐quadruplex (G‐quadruplex) characterization. We observe that G‐rich sequences fluoresce more strongly than duplex or single‐stranded DNA but much more weakly than fluorophores like fluorescein. This increase in the intrinsic fluorescence is not due to an increase in absorption at the excitation wavelength but rather to a change in the quantum yield. We show that unlabeled oligonucleotides that form G‐quadruplexes can be differentiated on the basis of their emission spectra from similar sequences that do not contain consecutive guanines. Intermolecular quadruplexes formed by the oligonucleotides 5′‐T4GnT4‐3′ (n = 4–10) display a nonlinear, but continuous, increase in emission intensity as the G content increases. The sequence 5′‐GGGT‐3′, which has been proposed to form a monomeric quadruplex and an interlocked quadruplex (Krishnan‐Ghosh et al. J Am Chem Soc 2004, 126, 11009), was compared with the similar sequence 5′‐TGGG‐3′, the structure of which has not been characterized. Both the maximum emission intensity and the spectral shape differ for these oligonucleotides as a function of sample preparation, indicating that different types of quadruplexes form for both sequences. Our work is the first to demonstrate that the suprastructure of G‐rich sequences can be probed using fluorescence signatures of unmodified oligonucleotides. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 841–850, 2009.This article was originally published online as an accepted preprint. The ”Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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Section: Discussionmentioning

confidence: 63%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Fluorescence of unmodified oligonucleotides: A tool to probe G‐quadruplex DNA structure

Méndez

Szalai

2009

Biopolymers

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“…1,2 Solvent effects on the photochemistry of nucleotide bases have been widely studied. In particular, the high sensitivity of the excited states of uracil to a solvent has made it a popular system for studying photochemistry.…”

Section: Introductionmentioning

confidence: 99%

Solvent-Induced Shifts in Electronic Spectra of Uracil

et al. 2011

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Highly accurate excitation spectra are predicted for the low-lying n−π* and π−π* states of uracil for both the gas phase and in water employing the complete active space self-consistent field (CASSCF) and multiconfigurational quasidegenerate perturbation theory (MCQDPT) methods. Implementation of the effective fragment potential (EFP) solvent method with CASSCF and MCQDPT enables the prediction of highly accurate solvated spectra, along with a direct interpretation of solvent shifts in terms of intermolecular interactions between solvent and solute. Solvent shifts of the n−π* and π−π* excited states arise mainly from a change in the electrostatic interaction between solvent and solute upon photoexcitation. Polarization (induction) interactions contribute about 0.1 eV to the solvent-shifted excitation. The blue shift of the n−π* state is found to be 0.43 eV and the red shift of the π−π* state is found to be −0.26 eV. Furthermore, the spectra show that in solution the π−π* state is 0.4 eV lower in energy than the n−π* state. Disciplines Chemistry CommentsThis article

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“…The excited-state dynamics of nucleic acid bases has gained much attention recently. 17 The problem is important because of the biological significance of the bases. These bases are the dominant chromophores in nucleic acids, and their photochemical and photophysical properties are implicated in the behavior of the nucleic acids upon irradiation.…”

Section: Introductionmentioning

confidence: 99%

Three-State Conical Intersections in Nucleic Acid Bases

2005

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The involvement of three-state conical intersections in the photophysics and radiationless decay processes of the nucleobases has been investigated using multireference configuration interaction methods. Three-state conical intersections have been located for the pyrimidine base, uracil, and the purine base, adenine. In uracil, a three-state degeneracy between the S 0 , S 1 , and S 2 states has been located at 6.2 eV above the ground-state minimum energy. This energy is 0.4 eV higher than vertical excitation to S 2 and at least 1.3 eV higher than the two-state conical intersections found previously. In adenine, two different three-state degeneracies between the S 1 , S 2 , and S 3 states have been located at energies close to the vertical excitation energies. The energetics of these three-state conical intersections suggest they can play a role in a radiationless decay pathway present in adenine. The existence of two different seams of three-state conical intersections indicates that these features are common and complicate the potential energy surfaces of adenine and possibly many other aromatic molecules.

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Ultrafast Excited-State Dynamics in Nucleic Acids

Cited by 1,214 publications

References 343 publications

Fluorescence of unmodified oligonucleotides: A tool to probe G‐quadruplex DNA structure

Fluorescence of unmodified oligonucleotides: A tool to probe G‐quadruplex DNA structure

Solvent-Induced Shifts in Electronic Spectra of Uracil

Three-State Conical Intersections in Nucleic Acid Bases

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