Models for DNA backbone motions: an interpretation of NMR relaxation experiments

Keepers, Joe W.; James, Thomas Leroy

doi:10.1021/ja00368a002

Cited by 89 publications

(50 citation statements)

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“…DISCUSSION A finding from this study is that each of the torsion angles (p', W', co, op, and qi may adopt any of the three conformational ranges g-, t, or g' without a substantial cost in energy relative to the standard B-DNA-like structure (with the exception of go' = g'); compensating changes occur in the other torsion angles such that the spatial arrangement of the bases is not disrupted. These conclusions support our 13C NMR-based observation that the DNA backbone possesses substantially greater motional freedom than the base pair moiety (15) and resolve the apparent paradox of"rigid double-helical DNA' found in hydrodynamic studies (16) and "very flexible double-helical DNA" found in spectroscopic studies (1,3).…”

Section: D(c-g-c-g-a-a-t-t-c-g-cmentioning

confidence: 44%

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Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings

Keepers

Kollman

Weiner

et al. 1982

Proc. Natl. Acad. Sci. U.S.A.

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G)]2 and [d(A)]12 [d(T)]12.Each ofthe backbone torsion angles (*, So, wo, o', jo') has been "forced" to alternative values from the normal B-DNA values (g+, t, g-, g-, t conformations). Compensating torsion angle changes preserve most of the base stacking energy in the double helix. In a second part of the study, one purine N3-pyrimidine NI distance at a time has been forced to a value of 6 A in an attempt to simulate the base opening motions required to rationalize proton exchange data for DNA. When the 6-A constraint is removed, many of the structures revert to the normal Watson-Crick hydrogen-bonded structure, but a number are trapped in structures ==5 kcal/mol higher in energy than the starting B-DNA structure. The relative energy ofthese structures, some of which involve a non-Watson-Crick thymine C2(carbon-

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Section: D(c-g-c-g-a-a-t-t-c-g-cmentioning

confidence: 44%

“…Sci. USA 79 (1982) 5541 qualitatively consistent with the models used to interpret NMR relaxation results (3).…”

Section: D(c-g-c-g-a-a-t-t-c-g-cmentioning

confidence: 45%

Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings

Keepers

Kollman

Weiner

et al. 1982

Proc. Natl. Acad. Sci. U.S.A.

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“…The question we address now is: What energy profile is followed during pseudorotation? In solution, the N S S interconversion occurs in periods of several nanoseconds [29]. One can expect the rotation of the (3')-OH group to be much more rapid ( 10-'-10 " s for disordered OH groups of oligosaccharides in the crystalline statethe molecular dynamics simulation data [ 361).…”

Section: Resultsmentioning

confidence: 42%

Ab initio calculations on the barrier to pseudorotation of model 2′‐deoxyfuranose and 2′‐deoxy‐2′‐fluorofuranose rings

Lesyng¹,

Marck²,

Guschlbauer³

1985

Int J of Quantum Chemistry

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Model ring systems 2'-deoxy-2'-fluororibofuranose and deoxyribofuranose have been investigated using ab iniiio calculations with the 3-21G basis set. The energy barrier to pseudorotation between the N and S states has been evaluated lor the three preferred orientations of the (3')-OH group. Positions of the energy minima and the transition state have k e n optimized with respect to the (3')-OH orientation. The barrier to pseudorotation of 2'-deoxy-2'-fluorofuranose is high and asymmetrical (A&+ = 20, A€,.+, i = 8 kJ/mol). whereas the barrier of 2'-deoxyfurdnose is lower and almost symmetrical (A€ i= 11-12 kJ/mol). The results obtained show that the preferred configuration of the 2'-deoxy-2'-fluororibofuranose (N state) is stabilized by an internal 0(3')-H. . . F interaction in accord with the crystallographic data.

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“…We believe our approach circumvents this difficulty in a straightforward manner. Kollman's observation (40,41) that there is only a weak coupling between the displacements of the bases and the displacements of the backbone supports our separation of base-base and backbone effects.…”

Section: Discussionmentioning

confidence: 49%

A molecular mechanical model to predict the helix twist angles of B-DNA

Tung

Harvey

1984

Nucl Acids Res

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We present here a model for the prediction of helix twist angles in B-DNA, a model composed of a collection of torsional springs. Statistically averaged conformational energy calculations show that, for a specified basepair step, the basepair-basepair conformational energy is quadratically dependent on the helix twist angle, so the calculations provide the spring parameters for the basepair-basepair interactions. Torsional springs can also be used to model the effects of the backbone on the helix twist, and the parameters for those springs are derived by fitting the model to experimental data. The model predicts a macroscopic torsional stiffness and a longitudinal compressibility (Young's modulus) which are both in good agreement with experiment. One biological consequence of the model is examined, the sequence specificity of the Eco RI restriction endonuclease, and it is shown that the discriminatory power of the enzyme receives a substantial contribution from the energetic cost of torsional deformations of the DNA when wrong sequences are forced into the enzyme binding site.

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Models for DNA backbone motions: an interpretation of NMR relaxation experiments

Cited by 89 publications

References 2 publications

Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings

Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings

Ab initio calculations on the barrier to pseudorotation of model 2′‐deoxyfuranose and 2′‐deoxy‐2′‐fluorofuranose rings

A molecular mechanical model to predict the helix twist angles of B-DNA

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