Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments

Nielsen, Lisbeth Munksgaard; Hoffmann, Søren Vrønning; Nielsen, Steen Brøndsted

doi:10.1039/c2cc35201j

Cited by 14 publications

(18 citation statements)

References 36 publications

(47 reference statements)

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“…In this study, we have investigated the photodimer formation in short thymine single strands T n with n = 2–7, 10, 11 by analyzing the observed changes in absorption and circular dichroism (CD) induced by exposure to 254 nm light. Synchrotron radiation for CD experiments was used to obtain information in the vacuum ultraviolet (VUV) ; this is particularly relevant for the photodimers that have blueshifted absorption due to lower π ‐electron delocalization. These experiments were done with the ASTRID storage ring facility located in Aarhus.…”

Section: Introductionmentioning

confidence: 99%

On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA

Baggesen

Hoffmann

Nielsen

2013

Photochem & Photobiology

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Solar light leads to thymine dimers that are mutagenic and primary cause of skin cancer. Here, we report absorption and synchrotron radiation circular dichroism (CD) spectra of Tn single strands with different number n of bases (n = 2-7, 10, 11) recorded after various 254 nm irradiation times. From a principal component analysis of the CD spectra, we extract fingerprint spectra of both the cyclobutane pyrimidine dimer (CPD) and the pyrimidine (6-4) pyrimidone photoadduct (64PP). Extending the CD measurements to the vacuum ultraviolet region in combination with systematic examinations of size effects is a new approach to gain insight on the dimeric photoproducts. We find a simple linear correlation between n and average number of dimers formed after 1 h of irradiation. The probability for a thymine to engage in a dimer increases from 32% for n = 2 to 41% for n = 11, which implies limited effects of terminal thymines, i.e., the reaction does not occur preferentially at the extremities of the single strands as previously stated. It is even possible to form two dimers with only two bridging thymines. Finally, experiments conducted on calf thymus DNA provided a similar signature of the photodimer, but differences are also evident.

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Section: Introductionmentioning

confidence: 99%

On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA

Baggesen

Hoffmann

Nielsen

2013

Photochem & Photobiology

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“…Moreover, a series of circular dichroism experiments [37,192,193] showed that the initial excitation in DNA homopolymers (adenine, thymine, and cytosine) generates excitons limited to only two bases, while the exciton extends over more bases in RNA homopolymers (adenine). It is noteworthy that the simple dinucleotide 2 0 -deoxyadenylyl(3 0 !…”

Section: Summary Of Experimental Resultsmentioning

confidence: 99%

Computational Modeling of Photoexcitation in DNA Single and Double Strands

Lü

Lan

Thiel

2014

Topics in Current Chemistry

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The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

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“…and Holm, A. I. et al . systematically investigated the contributions of the base composition and sequence to the VUVCD spectra of various types of DNA down to 175 nm [21,143,144,150]. They clarified the spectral characteristics of strands of polynucleotides composed of four bases as a function of strand length.…”

Section: Structural Analysis Of Nucleic Acidsmentioning

confidence: 99%

Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview

Gekko

2019

BIOPHYSICS

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Circular dichroism spectroscopy is widely used for analyzing the structures of chiral molecules, including biomolecules. Vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy using synchrotron radiation can extend the short-wavelength limit into the vacuum-ultraviolet region (down to ~160 nm) to provide detailed and new information about the structures of biomolecules in combination with theoretical analysis and bioinformatics. The VUVCD spectra of saccharides can detect the high-energy transitions of chromophores such as hydroxy and acetal groups, disclosing the contributions of inter- or intramolecular hydrogen bonds to the equilibrium configuration of monosaccharides in aqueous solution. The roles of hydration in the fluctuation of the dihedral angles of carboxyl and amino groups of amino acids can be clarified by comparing the observed VUVCD spectra with those calculated theoretically. The VUVCD spectra of proteins markedly improves the accuracy of predicting the contents and number of segments of the secondary structures, and their amino acid sequences when combined with bioinformatics, for not only native but also nonnative and membrane-bound proteins. The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in comparative analyses of synthetic poly-nucleotides composed of selected bases. This review surveys these recent applications of synchrotron-radiation VUVCD spectroscopy in structural biology, covering saccharides, amino acids, proteins, and nucleic acids.

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Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments

Cited by 14 publications

References 36 publications

On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA

On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA

Computational Modeling of Photoexcitation in DNA Single and Double Strands

Synchrotron-radiation vacuum-ultraviolet circular dichroism spectroscopy in structural biology: an overview

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