Structure of poly 8-bromoadenylic acid: conformational studies by CPF energy calculations

Govil, Girjesh; Fisk, Cherie L.; Howard, Frank B.; Miles, H. Todd

doi:10.1093/nar/4.8.2573

Cited by 22 publications

(15 citation statements)

References 35 publications

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“…In addition, the readers' attention is drawn to a few recent publications selected out of a vast literature concerning theoretical investigations on polynucleotide conformation (794)(795)(796)(797)(798)(799)(800)(801)(802)(803)(804)(805)(806)(807)(808), the flexibility ofthe double helix (809)(810)(811)(812)(813)(814)(815)(816)(817), and spectroscopic investigations of polynucleotide structures (818)(819)(820)(821)(822)(823)(824). The biochemical structure-function correlations are treated in reviews for DNA (792) and for RNA (793).…”

Section: Polymorphism Of Dna Versus Structural Conservatism Of Rna: Cmentioning

confidence: 99%

Principles of Nucleic Acid Structure

Saenger

1984

Springer Advanced Texts in Chemistry

5,985

312

6,279

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Section: Polymorphism Of Dna Versus Structural Conservatism Of Rna: Cmentioning

confidence: 99%

Principles of Nucleic Acid Structure

Saenger

1984

Springer Advanced Texts in Chemistry

5,985

312

6,279

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“…Recently studies using multidimensional function minimization procedure were made on the nucleic acid systems (Broyde et al, 1975;1978;Broyde and Hingerty, 1979;Fujii and Tomita, 1976;Kister and Dashevsky, 1976;Govil et al, 1977;Thiyagarajan and Ponnuswamy, 1978a, 1978bZhurkin et al, 1978;Levitt, 1978). These studies brought out many interesting aspects of the influence of the bases in the dimer, their actual sequence on the preferred backbone conformations and base stacking properties.…”

Section: Introductionmentioning

confidence: 99%

Conformational characteristics of the dimeric subunits of DNA from energy minimization studies. Mixed sugar-puckered dApdA, dApdT, dTpdA, and dTpdT

Ponnuswamy¹,

Thiyagarajan²

1981

Biophysical Journal

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An extensive investigation on the conformational characteristics of four deoxydinucleoside monophosphates, namely, dApdA, dApdT, dTpdA, and dTpdT was carried through calculation of the classical potential energy of the systems. The four major types of sugar-pucker sequences, namely, 3E-3E, 3E-2E, 2E-3E, 2E-2E, were included in the study. For each of the units, energies were computed for 96 starting conformations that resulted from the consideration of all possible low energy regions for the relevant seven dihedral angles and the four sugar-pucker sequences, and minimized by permitting all the seven dihedral angles to vary simultaneously. The number and the order of preference of low energy conformations obtained were found to be characteristic of the base sequence of the unit considered. The conformational states close to the A-DNA, B-DNA, C-DNA, and Watson-Crick DNA structures are noted to be preferred for all the units except dTpdT. The 3E-2E sugar-pucker sequence is the most favored and the 2E-3E sequence is the least favored state in terms of the associated number of local minima. For each unit, there exists a set of specific conformational states with more or less equal stabilities but different sugar-pucker sequences. The mixed sugar-pucker states 2E-3E and 3E-2E, when incorporated, in the conventional A-DNA and B-DNA conformational states, respectively, have energies that allow them to act as intermediates in the B form in equilibrium with A form transitions. Such transitions are most likely to occur at sites with a Thymine-Adenine base sequence. Available experimental results were interpreted in terms of their stabilities.

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“…An earlier investigation (28) of the energetic relationship between a and y in DNA produced maps which predicted the linear correlation between these angles, but picked a::::: 180° to be most stable and did not indicate the minimum at(a=60o, y= 180°). A semi-linear correlation between a andy has also been predicted in maps calculated using only base stacking as a measure of the relative favorablenesses of various conformations (30), supporting the hypothesis that this correlation is an example of the crankshaft effect ~-a Undoubtedly, the most widely studied nucleic acid torsion angle dependence is that between the two P-0 backbone torsions~ (C3'-03'-P-05') and a (03'-P-05'-C5') (15,16,18,20,(22)(23)(24)(25)(26)(27)(28)(29)(34)(35)(36)(37)(38)(39)(40).Thisisaconsequenceofthebeliefthatmuchoftheconformational flexibility of nucleic acids stems from variation in this pair of angles (62,(70)(71)(72). The maps produced in this study are shown in Figure 2h.…”

Section: ~-Ementioning

confidence: 68%

“…Both classical (12,13,15,16,(18)(19)(20)22,(24)(25)(26)(27)(28)(29) and quantum mechanical (34)(35)(36)(37)(38)(39)(40) techniques have been used to evaluate the conformational energies. Oligonucleotide maps fora-y (28) and y-x (17 ,19) have also been reported, but for a large majority of the possible pairs (15 out of 21), including several of particular interest, no maps have heretofore been published.…”

Section: The Energy Contour Maps: Comparison With Previous Calculationsmentioning

confidence: 99%

Conformational Studies of Nucleic Acids: IV. The Conformational Energetics of Oligonucleotides: d(ApApApA) and ApApApA

Pearlman

Kim²

1986

Journal of Biomolecular Structure and Dynamics

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Utilizing a new method for modeling furanose pseudorotation (D. A. Pearlman and S.-H. Kim, J. Biomol. Struct. Dyn. 3, 85 (1985)) and the empirical multiple correlations between nucleic acid torsion angles we derived in the previous report (D. A. Pearlman and S.-H. Kim, previous paper in this issue), we have made an energetic examination of the entire conformational spaces available to two nucleic acid oligonucleotides: d(ApApApA) and ApApApA. The energies are calculated using a semi-empirical potential function. From the resulting body of data, energy contour map pairs (one for the DNA molecule, one for the RNA structure) have been created for each of the 21 possible torsion angle pairs in a nucleotide repeating unit. Of the 21 pairs, 15 have not been reported previously. The contour plots are different from those made earlier in that for each point in a particular angle-angle plot, the remaining five variable torsion angles are rotated to the values which give a minimum energy at this point. The contour maps are overall quite consistent with the experimental distribution of oligonucleotide data. A number of these maps are of particular interest: delta (C5'-C4'-C3'-O3')-chi (O4'-C1'-N9-C4), where the energetic basis for an approximately linear delta-chi correlation can be seen: zeta (C3'-O3'-P-O5')-delta, in which the experimentally observed linear correlation between zeta and delta in DNA(220 degrees less than zeta less than 280 degrees) is clearly predicted; zeta-epsilon (C4'-C3'-O3'-P), which shows that epsilon increases with decreasing zeta less than 260 degrees; alpha (O3'-P-O5'-C5')-gamma (O5'-C5'-C4'-C3') where a clear linear correlation between these angles is also apparent, consistent with experiment; and several others. For the DNA molecule studied here, the sugar torsion delta is predicted to be the most flexible, while for the RNA molecule, the greatest amount of flexibility is expected to reside in alpha and gamma. Both the DNA and RNA molecules are predicted to be highly polymorphic. Complete energy minimization has been performed on each of the minima found in the energy searches and the results further support this prediction. Possible pathways for B-form to A-form DNA interconversion suggested by the results of this study are discussed. The results of these calculations support use of the new sugar modeling technique and torsion angle correlations in future conformational studies of nucleic acids.

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Structure of poly 8-bromoadenylic acid: conformational studies by CPF energy calculations

Cited by 22 publications

References 35 publications

Principles of Nucleic Acid Structure

Principles of Nucleic Acid Structure

Conformational characteristics of the dimeric subunits of DNA from energy minimization studies. Mixed sugar-puckered dApdA, dApdT, dTpdA, and dTpdT

Conformational Studies of Nucleic Acids: IV. The Conformational Energetics of Oligonucleotides: d(ApApApA) and ApApApA

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