Conformations of Nicked and Gapped DNA Structures by NMR and Molecular Dynamic Simulations in Water

Roll, Claus; Ketterlé, Christophe; Faibis, Valérie; Fazakerley, and G. Victor; Boulard, Yves

doi:10.1021/bi972377w

Cited by 71 publications

(87 citation statements)

References 48 publications

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“…This challenge can be addressed by a combination of experimental approaches and molecular dynamics simulations. In recent years, a significant number of molecular dynamics studies [23][24][25][26][27][28][29][30] on DNA and RNA systems have appeared. Cheatham & Kollman reviewed molecular dynamics simulations of nucleic acids from 1995 to 2000, discussing force fields for nucleic acids and simulation protocols using explicit solvent and counterions.…”

Section: Introductionmentioning

confidence: 99%

Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

et al. 2009

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We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water., Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA -namely major groove width, inclination and the number of base pairs in a helical twist -over a 30ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors).

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Section: Introductionmentioning

confidence: 99%

Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

et al. 2009

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“…On the experimental side, Protozanova et al have measured free energy of stacking for base-pair steps in a nicked DNA duplex (Protozanova et al 2004). It is attractive to generalise these stacking-free energies for nicked DNA to the intact DNA double helix; however, NMR analyses have shown that the broken phosphodiester bond pushes the conformation away from canonical B-form (Pieters et al 1989;Roll et al 1998; Snowden-Ifft & Wemmer, 1990) which leaves . Overall then, while there is significant disagreement on the magnitude (and sometimes the ranking) of the 10 stacking energies for complementary base-pair steps, the key feature of a weak CG stack which points to the existence of a GNC triplet code is preserved.…”

Section: −1mentioning

confidence: 99%

DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase

Taghavi

Schoot

Berryman

2017

Quart. Rev. Biophys.

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Abstract. Using atomistic simulations, we show the formation of stable triplet structure when particular GC-rich DNA duplexes are extended in solution over a timescale of hundreds of nanoseconds, in the presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a possible solution phase of the double helix under tension, subject to sequence and the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base pairs as the first step of operation of recombinase enzymes like RecA, we emphasise the structure-function relationship in Σ DNA. We supplement atomistic calculations with thermodynamic arguments to show that codons for 'phase 1' amino acids (those appearing early in evolution) are more likely than a lower entropy GC-rich sequence to form triplets under tension. We further observe that the four amino acids supposed (in the 'GADV world' hypothesis) to constitute the minimal set to produce functional globular proteins have the strongest triplet-forming propensity within the phase 1 set, showing a series of decreasing triplet propensity with evolutionary newness. The weak form of our observation provides a physical mechanism to minimise read frame and recombination alignment errors in the early evolution of the genetic code.

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“…The convolution in (8) is a convolution defined on SE(3). Letting g and h denote any group elements in SE(3), and letting f a (g) and f b (g) be two arbitrary functions defined on SE(3), the convolution on SE(3) is defined as 51 (10) where the little circle is the group multiplication operator for rigid-body motions. Equation (8) can be extended further to solve the multi-joint case by convolving more PDFs of involved segments and joints.…”

Section: General Ideamentioning

confidence: 99%

“…The bending angle caused by a single gap was estimated at around 12°. Roll et al reported a fluctuating bending angle centered around 17° at the nick site of DNA based on nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations 10 . Kahn et al studied the bending and flexibility induced by symmetric internal loops by gel electrophoresis experiments and cyclization kinetics analysis, and found that the internal loop induced high local isotropic flexibility 11 .…”

Section: Introductionmentioning

confidence: 99%

Conformational Statistics of Semiflexible Macromolecular Chains with Internal Joints

Chirikjian

2006

Macromolecules

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Fluctuations in the bending angles at internal irregularities of DNA and RNA (such as symmetric loops, bulges, and nicks/gaps) have been observed from various experiments. However, little effort has been made to computationally predict and explain the statistical behavior of semiflexible chains with internal defects. In this paper, we describe the general structure of these macromolecular chains as inextensible elastic chains with one or more internal joints which have limited ranges of rotation, and propose a method to compute the probability density functions of the end-to-end pose of these macromolecular chains. Our method takes advantage of the operational properties of the non-commutative Fourier transform for the group of rigid-body motions in three-dimensional space, SE(3). Two representative types of joints, the hinge for planar rotation and the ball joint for spatial rotation, are discussed in detail. The proposed method applies to various stiffness models of semi-flexible chain-like macromolecules. Examples are calculated using the Kratky-Porod model with specified stiffness, angular fluctuation, and joint locations. Entropic effects associated with internal angular fluctuations of semi-flexible macromolecular chains with internal joints can be computed using this formulation. Our method also provides a potential tool to detect the existence of internal irregularities.

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Conformations of Nicked and Gapped DNA Structures by NMR and Molecular Dynamic Simulations in Water

Cited by 71 publications

References 48 publications

Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase

Conformational Statistics of Semiflexible Macromolecular Chains with Internal Joints

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