A standard reference frame for the description of nucleic acid base-pair geometry

Olson, Wilma K.; Bansal, Manju; Burley, S.K.; Dickerson, Richard E.; Gerstein, Mark; Harvey, Stephen C.; Heinemann, Udo; Lu, Xiang‐Jun; Neidle, Stephen; Shakked, Zippora; Sklenar, Heinz; Suzuki, Masashi; Tung, Chang‐Shung; Westhof, Éric; Wolberger, Cynthia; Berman, Helen M.

doi:10.1006/jmbi.2001.4987

Cited by 529 publications

(420 citation statements)

References 36 publications

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“…Again, in [39] we find a well-posed definition. Starting from the segment connecting the C1 atoms for each base pair, the midpoint of this is then connected to the above point that defines the DNA centre line at the same base pair (see figure 1(C) , which realign such vectors to the z-axis.…”

Section: Geometrical Calculationsmentioning

confidence: 56%

“…To do so, we followed the prescriptions of [39] and defined the centre line as the line connecting the mid-points of the segment that, for each base pair, connects the purine C8 and pyrimidine C6 atoms. We then computed the average vector connecting these points, which defines the vectors a 1 ( ) and a 2 ( ) , the centre-line directions of DNA 1 and DNA 2, respectively.…”

Section: Geometrical Calculationsmentioning

confidence: 99%

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The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

Cortini

Cheng

Smith

2017

J. Phys.: Condens. Matter

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Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning's theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of k T 1 B . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.

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Section: Geometrical Calculationsmentioning

confidence: 56%

Section: Geometrical Calculationsmentioning

confidence: 99%

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

Cortini

Cheng

Smith

2017

J. Phys.: Condens. Matter

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“…54 To resolve the numerical discrepancies, in 1999, the Tsukuba Workshop on nucleic acid structure and interactions reached an agreement with "a standard reference frame for the description of nucleic acid base-pair geometry". 56 In accord with this, the 3DNA program with this standard reference frame is utilized for the data analysis below.…”

Section: Resultsmentioning

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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“…The list of pdb files deposited in Nucleic Acid Database [33,34] that were used in this study as the source of structural parameters of dinucleotide steps. First two columns comprise B-DNA codes according to NDB and PDB identification styles.…”

Section: Table S1mentioning

confidence: 99%

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Cysewski

2010

J Mol Model

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Non-additivity of base-base interactions in all ten possible model dinucleotide steps were analyzed on MP2/aug-cc-pvDZ quantum chemistry level. Selected conformations of four nucleobases exactly matched to ones occurring in B-DNA crystals. In most of 162 analyzed tetramers both threeand four-body contributions are negligible except of d(GpG) steps. However, in these dinucleotides both contributions are always of opposite signs and in all cases the sum of all non-additive part of intermolecular interactions do not exceed 2.6 kcal/mol. This stands for less than 5% of the overall binding energy of dinucleotide steps. Also replacements of guanine with 8-oxoguanine in d(GpG) systems introduces non-additivity of the same magnitude as for canonical dinucleotides. It is observed linear relationships between values of the total binding energy obtained in the tetramer basis set and estimated energy exclusively in dimers basis sets with assumption of pairwise additivities. For all analyzed dinucleotides steps there are also linear correlations between amount of non-additive contributions and magnitude of pairs interactions. Based on differences in electrostatic contribution to the total binding energy of four nucleobases and polarity of dinucleotide steps three distinct classes of dinucleotide steps were identified.Response to Reviewers: 1) I recommend to do a careful proofreading, there are many typos and some sentences are difficult to understand. Thank you. Careful proofreading was applied and text was modified accordingly.2) Page 3, Results and discussion Alltogether 162 dinucleotide steps were analyzed. The number of individual steps is variable, why is it so? Why there was 48 d(GpG) steps, but only 10 d(GpC) steps? What were the PDB codes of structures from which steps were chosen, and which steps (chain ID, res ID) were chosen? What was the resolution of these structures? This information could go to the Supplementary material.In supplementary material details related to analyzed structures are provided now. The differences in dinucleotide populations have strictly technical reason. Since in my previous work accepted for publication in Int.J.Quantum Chem. (DOI:10.1002/qua.22435) detailed analysis of d(GpG) steps were presented I have just included these data in this work. Consequently this dinucleotide is overrepresented. Since it constitutes its own class I do not think that such overrepresentation changes papers conclusions. On the other hand it is not necessary extending the number of other dinucleotide steps since the non-additivity is quite small and they were selected from broad range of data according to IIE and structural parameters diversities.3) Page 3, Results and discussion The numbers of steps are large enough to perform some statistical analysis of resulting energies. E.g. ANOVA could be performed to test whether the mean energies in dinucleotide steps differ significantly each from other. Also, is the distribution of energies for individual steps Gaussian or not? If not, some non-parametric ...

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A standard reference frame for the description of nucleic acid base-pair geometry

Cited by 529 publications

References 36 publications

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

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

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

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