Structure and Dynamics of Poly(T) Single-Strand DNA:  Implications toward CPD Formation

Johnson, Andrew T.; Wiest, Olaf

doi:10.1021/jp076371k

Cited by 59 publications

(76 citation statements)

References 41 publications

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“…The conformational range for thymine dimerization is not quite understood. Theoretical QM studies predict that the CI can be reached at d<3.6-4 Å 20,68 , which is close to the empirical estimations of MD simulation 32,33,68 . MD simulations also predict the cut-off for dihedral angle to be 30-50°.…”

Section: Resultssupporting

confidence: 79%

Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

2015

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Direct DNA absorption of UVB photons in a spectral range of 290-320 nm of terrestrial solar radiation is responsible for formation of cyclobutane pyrimidine dimers causing skin cancer. Formation of UVB-induced lesions is not random, and conformational features of their hot spots remain poorly understood. We calculated the electronic excitation spectra of thymine, cytosine, and adenine stacked dimers with ab initio methods in a wide range of conformations derived from PDB database and molecular dynamics trajectory of thymine-containing oligomer. The stacked dimers with reduced interbase distances in curved, hairpin-like, and highly distorted DNA and RNA structures exhibit excitonic transitions red-shifted up to 0.6 eV compared to the B-form of stacked bases, which makes them the preferred target for terrestrial solar radiation. These results might have important implications for predicting the hot spots of UVB-induced lesions in nucleic acids.

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Section: Resultssupporting

confidence: 79%

Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

2015

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“…Possible explanations for the increased yield of Gh in ssODNs requires understanding how the ODN context affects the common hydantoin intermediate, 5-HO-OG. Context effects that are not observed in the nucleoside include: (1) Steric effects from adjacent bases (i.e., base stacking), 74 or (2) electrostatics, due to the anionic sugar-phosphate backbone in ODNs. 75 To study the base stacking influence on OG-oxidation products, reactions were conducted at 4.0 °C.…”

Section: Resultsmentioning

confidence: 99%

Structural Context Effects in the Oxidation of 8-Oxo-7,8-dihydro-2′-deoxyguanosine to Hydantoin Products: Electrostatics, Base Stacking, and Base Pairing

et al. 2012

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8-Oxo-7,8-dihydroguanine (OG) is the most common base damage found in the cell where it resides in many structural contexts including the nucleotide pool, single-stranded DNA at transcription forks and replication bubbles, and in duplex DNA base paired with either A or C. OG is prone to further oxidation to the highly mutagenic hydantoin products, spiroiminodihydantoin (Sp) and 5-guanidinohydantoin (Gh) in a sharply pH-dependent fashion within nucleosides. In the present work, studies were conducted to determine how the structural context affects OG oxidation to the hydantoins. These studies revealed a trend in which the Sp yield was greatest in unencumbered contexts, such as nucleosides, while the Gh yield increased in oligodeoxynucleotide (ODN) contexts or at reduced pH. Oxidation of oligomers containing hydrogen bond modulators (2,6-diaminopurine, N4-ethylcytidine) or alteration of the reaction conditions (pH, temperature, and salt) identify base stacking, electrostatics and base pairing as the drivers of the key intermediate 5-hydroxy-8-oxo-7,8-dihydroguanine (5-HO-OG) partitioning along the two hydantoin pathways, allowing us to propose a mechanism for the observed base pairing effects. Moreover, these structural effects cause an increase in the effective pKa of 5-HO-OG following an increasing trend from 5.7 in nucleosides to 7.7 in a duplex bearing an OG•C base pair, which supports the context-dependent product yields. The high yield of Gh in ODNs underscores the importance of further study on this lesion. The structural context of OG also determined its relative reactivity toward oxidation for which the OG•A base pair is ~2.5-fold more reactive than an OG•C base pair, and with the weak one-electron oxidant ferricyanide, the OG nucleoside reactivity is >6000-fold greater than that of OG•C in a duplex, leading to the conclusion that OG in the nucleoside pool should act as a protective agent for OG in the genome.

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“…[6][7][8][9] The most abundant UV induced DNA lesions occur between thymine bases, and all-thymine single strands became the focus of a series of time resolved experimental and computational studies. [10][11][12][13][14][15][16][17] Thereby, charge transfer (CT) states have been suggested to act as precursor species for the formation of (6-4) photoproducts in thymine sequences. 17 Yet, until now charge transfer excited states between two thymine bases have not been identified unequivocally.…”

mentioning

confidence: 99%

Identification of charge separated states in thymine single strands

et al. 2014

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Structure and Dynamics of Poly(T) Single-Strand DNA: Implications toward CPD Formation

Cited by 59 publications

References 41 publications

Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

Structural Context Effects in the Oxidation of 8-Oxo-7,8-dihydro-2′-deoxyguanosine to Hydantoin Products: Electrostatics, Base Stacking, and Base Pairing

Identification of charge separated states in thymine single strands

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