Base Sequence and Higher-Order Structure Induce the Complex Excited-State Dynamics in DNA

Schwalb, Nina K.; Temps, F.

doi:10.1126/science.1161651

Cited by 154 publications

(215 citation statements)

References 32 publications

Supporting

Mentioning

200

Contrasting

Unclassified

Order By: Relevance

“…G-rich sequences with contiguous guanines present significantly different intensities from homologous sequences containing interspersed Gs. 26,27 The general trends in the fluorescence spectra observed in our work are that (1) the fluorescence maximum wavelength is approximately the same in all of the spectra collected in the presence of K 1 and (2) some oligonucleotides present an additional shoulder at 390-395 nm in the presence of K 1 .…”

Section: Discussionsupporting

confidence: 57%

“…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%

“…26 The sequence d(G) 20 has been reported to have the highest average fluorescence lifetime (11.3 ps) out of a series of single-stranded and duplex oligonucleotides probed. 27 On the basis of this information, we demonstrate that emission from unmodified-oligonucleotides can be used to expand our understanding of the structure and properties of polymers rich in G, in particular, G-quadruplexes.…”

Section: Introductionmentioning

confidence: 86%

See 2 more Smart Citations

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

Méndez

Szalai

2009

Biopolymers

View full text Add to dashboard Cite

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

show abstract

Section: Discussionsupporting

confidence: 57%

Section: Discussionmentioning

confidence: 63%

Section: Introductionmentioning

confidence: 86%

See 1 more Smart Citation

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

Méndez

Szalai

2009

Biopolymers

View full text Add to dashboard Cite

show abstract

“…Adenine homopolymers and homoduplexes made of adenine-thymine base pairs show much slower decay times compared to those of isolated bases 1,2,47,48 . More recent findings support the fact that long lived excited states decay more rapidly in double-stranded poly(dA-dT) than in single stranded poly(dA) sequences 49,50 , addressing the role of inter-strand proton transfer in the deactivation mechanism 7,12,13 . Long-lived signals have also been probed by means of fluorescence up-conversion techniques 5,51,52 , and more recently through femtosecond infrared spectroscopy by probing the distinct cationic and anionic species formed in the process 10 .…”

Section: Introductionmentioning

confidence: 71%

“…12 and an imaginary shift of 0.2 a.u. 13 were used. Transition dipole moments were calculated at SA-CASSCF/RASSCF level.…”

Section: Reference Calculation For Adenine Monomer In Gas-phasementioning

confidence: 99%

Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations

et al. 2015

View full text Add to dashboard Cite

The SOS//QM/MM [Rivalta et al., Int. J. Quant. Chem. 2014, 114, 85.] method consists of an arsenal of computational tools allowing accurate simulation of onedimensional (1D) and bidimensional (2D) electronic spectra of monomeric and dimeric systems with unprecedented details and accuracy. Prominent features like doubly excited local and excimer states, accessible in multi-photon processes, as well as charge-transfer excimer states arise naturally through the fully quantum-mechanical description of the aggregates. In this contribution the SOS//QM/MM approach is extended to simulate time-resolved 2D spectra that can be used to characterize ultrafast excited state relaxation dynamics with atomistic details. We demonstrate how critical structures on the excited state potential energy surface, obtained through state-of-the-art quantum chemical computations, can be used as snapshots of the excited state relaxation dynamics to generate spectral fingerprints for different de-excitation channels. The approach is based on high-level multi-configurational wavefunction methods combined with non-linear response theory and incorporates the effects of the solvent/environment through hybrid quantum mechanics/molecular mechanics (QM/MM) techniques. Specifically, the protocol makes use of the second-order Perturbation theory (CASPT2) on top of Complete Active Space Self Consistent Field (CASSCF) strategy to compute the high-lying excited states that can be accessed in different 2D experimental setups. As an example, the photophysics of the stacked adenine-adenine dimer in a double-stranded DNA is modeled through 2D near-UV spectroscopy.

show abstract

Hydrogen Bonding Regulates the Monomeric Nonradiative Decay of Adenine in DNA Strands

2011

View full text Add to dashboard Cite

Deformationsverbot: Für Adenin in (dA)10 wird die innere Konversion zum Grundzustand durch eine konische S0/S1‐Überschneidung mit stark aus der Ebene herausgedrehter Aminogruppe bestimmt (links). In (dA)10⋅(dT)10 wird dieser Pfad durch die Bildung von Adenin‐Thymin‐Wasserstoffbrücken unterbunden (rechts). Für angeregtes Adenin in DNA‐Strängen werden zehnmal längere Lebensdauern berechnet als im Vakuum oder in Wasser.

show abstract

Base Sequence and Higher-Order Structure Induce the Complex Excited-State Dynamics in DNA

Cited by 154 publications

References 32 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

Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations

Hydrogen Bonding Regulates the Monomeric Nonradiative Decay of Adenine in DNA Strands

Contact Info

Product

Resources

About