Full-strand Minimization of Single and Double Stranded B-DNA Using Monte-Carlo Annealing

Sfyrakis, Konstantinos; Provata, A.; Povey, David C.; Howlin, Brendan J.

doi:10.1080/0892702021000008858

Cited by 1 publication

(3 citation statements)

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“…This reemphasizes the importance of long time scales for the simulation. While earlier simulations on the ∼5 ns time scale [18][19][20][21][22][23][24][25][26] found indications for the formation of hairpins, the results presented here indicate that they represent stable structures for ssDNA. It is noteworthy that the distances of 3% additive probability calculated from these simulations agree well with the literature data on π-π stacking interactions in systems prior to [2 + 2] cycloadditions.…”

Section: Resultscontrasting

confidence: 53%

“…Several groups have studied the dynamics of ssDNA, and the agreement between theory and experiment is promising. [19][20][21][22][23][24][25][26] Biyani and Nishigaki in 2005 used gel electrophoresis and molecular dynamics to study structural dynamics in solution. 26 In this work it was found that a high correlation exists between experiment and theory in the context of ssDNA folding.…”

Section: Introductionmentioning

confidence: 99%

“…Several groups have studied the dynamics of ssDNA, and the agreement between theory and experiment is promising. − Biyani and Nishigaki in 2005 used gel electrophoresis and molecular dynamics to study structural dynamics in solution …”

Section: Introductionmentioning

confidence: 99%

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

Johnson

Wiest

2007

J. Phys. Chem. B

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The formation of cyclobutane pyrimidine dimers between adjacent thymines by UV radiation is thought to be the first event in a cascade leading to skin cancer. Recent studies showed that thymine dimers are fully formed within 1 ps of UV irradiation, suggesting that the conformation at the moment of excitation is the determining factor in whether a given base pair dimerizes. MD simulations on the 50 ns time scale are used to study the populations of reactive conformers that exist at any given time in T18 single-strand DNA. Trajectory analysis shows that only a small percentage of the conformations fulfill distance and dihedral requirements for thymine dimerization, in line with the experimentally observed quantum yield of 3%. Plots of the pairwise interactions in the structures predict hot spots of DNA damage where dimerization in the ssT18 is predicted to be most favored. The importance of hairpin formation by intra-strand base pairing for distinguishing reactive and unreactive base pairs is discussed in detail. The data presented thus explain the structural origin of the results from the ultrafast studies of thymine dimer formation.

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