The Chirality of DNA: Elasticity Cross-Terms at Base-Pair Level Including A-Tracts and the Influence of Ionic Strength

Noy, Agnes; Golestanian, Ramin

doi:10.1021/jp104133j

Cited by 18 publications

(13 citation statements)

References 64 publications

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“…We saw above that solvent and ion force-field models, including both Na + Cl − or K + Cl − , had little impact on the global structure or flexibility of DDD. This may seem reasonable given the ‘physiological’ conditions range used in this work (see Noy and Golestanian ( 69 )). However, while simulations carried out with minimal (neutralizing) ionic strength seem to lead to shorter persistence lengths (Supplementary Table S6), there is no systematic trend relating flexibility and ionic strength.…”

Section: Resultssupporting

confidence: 59%

Long-timescale dynamics of the Drew–Dickerson dodecamer

et al. 2016

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We present a systematic study of the long-timescale dynamics of the Drew–Dickerson dodecamer (DDD: d(CGCGAATTGCGC)2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na+Cl− or K+Cl−. The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 μs) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 μs of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.

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Section: Resultssupporting

confidence: 59%

Long-timescale dynamics of the Drew–Dickerson dodecamer

et al. 2016

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“…The former result indicates that high-G$C DNA is harder to stretch than balanced A$T/G$C DNA (see Table 1) and the latter indicates that high-G$C DNA requires a higher energy to melt for a given loading rate than balanced A$T/G$C DNA. Both the stretch modulus and the melting behavior are associated with the magnitude of base-stacking and basepairing interactions (1,(40)(41)(42).…”

Section: Discussionmentioning

confidence: 99%

Mechanical Properties of High-G⋅C Content DNA with A-Type Base-Stacking

Hormeño

Ibarra

Carrascosa

et al. 2011

Biophysical Journal

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The sequence of a DNA molecule is known to influence its secondary structure and flexibility. Using a combination of bulk and single-molecule techniques, we measure the structural and mechanical properties of two DNAs which differ in both sequence and base-stacking arrangement in aqueous buffer, as revealed by circular dichroism: one with 50% G·C content and B-form and the other with 70% G·C content and A-form. Atomic force microscopy measurements reveal that the local A-form structure of the high-G·C DNA does not lead to a global contour-length decrease with respect to that of the molecule in B-form although it affects its persistence length. In the presence of force, however, the stiffness of high-G·C content DNA is similar to that of balanced-G·C DNA as magnetic and optical tweezers measured typical values for the persistence length of both DNA substrates. This indicates that sequence-induced local distortions from the B-form are compromised under tension. Finally, high-G·C DNA is significantly harder to stretch than 50%-G·C DNA as manifested by a larger stretch modulus. Our results show that a local, basepair configuration of DNA induced by high-G·C content influences the stretching elasticity of the polymer but that it does not affect the global, double-helix arrangement.

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“…Systems were energy-minimized, thermalized (T = 298 K) and equilibrated using standard protocols. 54,55 The final structures were subject to 1 ms of productive MD simulation at constant temperature (298 K) and pressure (1 atm) 56 using periodic boundary conditions, particle mesh Ewald 57 and an integration time step of 2 fs. 58 Principal component analysis was done with pyPcazip 59 and fast Fourier transforms were done with an in-house program written in python.…”

Section: Methodsmentioning

confidence: 99%