Conformations of double-helical nucleic acids

Khutorsky, V.; Poltev, V. I.

doi:10.1038/264483a0

Cited by 16 publications

(12 citation statements)

References 7 publications

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“…(12). Some interatomic distances were also considered if they corresponded to the van-der-Waals energy more than 0.4 kcal/mole though they were somewhat larger than the reduced interatomic contacts as defined in (12 ined from independent conformational parameters using an algorithm similar to that described earlier for regular double-helical polynucleotides (6 Conformations with the parameters of sugar-phosphate backbone and glycoside bond positions characteristic of regular polynucleotides consisting of A:U pairs are sterically allowed for the fragments containing coplanar uracyl and cytosine. The energy of such conformations is about 6 kcal/mole higher than for the most favourable conformations of fragments with U:C pairs, mainly owing to a worse interaction between U and C bases.…”

Section: Methodsmentioning

confidence: 99%

“…As in the case of regular double-stranded polynucleotides (6)(7)(8) parameters of DNA fragments containing mispairs…”

Section: Conformational Parameters Of Fragmentsmentioning

confidence: 99%

“…Theoretical conformational analysis of regular double-helical polynucleotides has shown that there are regions of minimum energy values of intramolecular interactions corresponding to A-and B-families of nucleic acid con-formations (6)(7)(8). Within these regions different mutual positions of the base pairs at rather close values of dihedral angles of the sugar-phosphate backbone are possible (8).…”

Section: Introductionmentioning

confidence: 99%

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Possible conformations of double-helical polynucleotides containing incorrect base pairs

Chuprina

Poltev

1983

Nucl Acids Res

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Theoretical conformational analysis using classical potential functions has shown the possibility of incorporation of nucleotide mispairs with the bases in normal tautcmeric forms into the DNA double helix. Incorrect purinepyrimidine, purine-purine and pyrimidine-pyrimidine pairs can be incorporated into the double helix existing both in A-and B-conformations. The most energy favourable conformations of fragments containing a mispair have all the dihedral angles of the sugar-phosphate backbone within the limits characteristic of double helices consisting of Watson-Crick nucleotide pairs. Incorporation of mispairs is possible practically without the appearance of reduced interatomic contacts. Mutual position of bases in the incorporated mispair does not differ much from their position at the energy minimum of the corresponding isolated base pairs. Conformational parameters of irregular regions of double-stranded polynucleotides containing G:U,

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Section: Methodsmentioning

confidence: 99%

“…As in the case of regular double-stranded polynucleotides (6)(7)(8) parameters of DNA fragments containing mispairs…”

Section: Conformational Parameters Of Fragmentsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Possible conformations of double-helical polynucleotides containing incorrect base pairs

Chuprina

Poltev

1983

Nucl Acids Res

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“…We have investigated in detail the interaction energy between pairs as a function of variables determining their position in the double helix [7,81. Such an investigation, besides being of particular interest by itself, allows one to drastically diminish the region of conformational space that should be investigated.…”

Section: Interaction Of Base Pairs In the Double Helicesmentioning

confidence: 98%

“…Therefore an algorithm was worked out and applied for the computations. It allows one to express the dihedral angles of the sugar-phosphate backbone and dependent bond angles of the sugar ring as functions of variables determining mutual position of base pairs and independent variables of the sugar ring [6].…”

Section: Choice Of Conformational Variablesmentioning

confidence: 99%

Conformational analysis of double‐helical polynucleotides

Khutorsky¹,

Poltev

1979

Int J of Quantum Chemistry

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The intramolecular interaction energy of the regular double-helical polynucleotide as a function of variables that determine the mutual position of base pairs and sugar pucker was calculated using atom-atom potentials. The calculations showed the existence of two valley-like regions with minimal values on the energetic surface. One of them corresponds to the A family of nucleic acids, the other to the B family. The points that correspond to the models constructed by means of x-ray data are placed in a conformational space near the lines that describe the position of the bottom of the valleys.

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Simulation of conformational possibilities of DNA via calculation of nonbonded interactions of complementary dinucleoside phosphate complexes

et al. 1981

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SynopsisUsing classical potential functions, we carried out potential-energy calculations on the complementary deoxydinucleoside phosphate complexes dApdA:dUpdU, dUpdA:dUpdA, and dApdU:dApdU. All dihedral and bond angles, except those of the nitrogen bases, were varied. The resulting minimum-energy conformations of the complexes are close to DNA A-and B-family conformations, with a typical arrangement of the nitrogen bases. The dihedral and bond angles of one of the molecules forming the complex can thereby differ by several degrees from those of the other molecule. For different base sequences, some dihedral and bond angles may vary over a range of several degrees without appreciably changing the total energy of the complex. Some low-energy conformations of the complexes corresponding to other regions of the conformational space are also found. The biological consequences of possible changes in dihedral and bond angles, occurring on interaction with other molecules, are discussed.

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Conformations of double-helical nucleic acids

Cited by 16 publications

References 7 publications

Possible conformations of double-helical polynucleotides containing incorrect base pairs

Possible conformations of double-helical polynucleotides containing incorrect base pairs

Conformational analysis of double‐helical polynucleotides

Simulation of conformational possibilities of DNA via calculation of nonbonded interactions of complementary dinucleoside phosphate complexes

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