Conformational studies of nucleic acids: IV. The conformational energetics of oligonucleotides: d(ApApApA) and ApApApA.

Journal of Biomolecular Structure & Dynamics
D A Pearlman, S H Kim

Abstract

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 appr...Continue Reading

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Citations

Jul 20, 1991·Journal of Molecular Biology·D A Pearlman, P A Kollman
Aug 1, 1996·Journal of Biomolecular Structure & Dynamics·E Fadrná, J Koca
Dec 20, 2002·Nucleic Acids Research·Péter VárnaiBrigitte Hartmann
Feb 3, 2004·Biopolymers·Shayantani Mukherjee, Dhananjay Bhattacharyya
Aug 1, 1986·Journal of Biomolecular Structure & Dynamics·D A Pearlman, S H Kim
Jan 21, 2010·Journal of Biomolecular Structure & Dynamics·Aditi BorkarDhananjay Bhattacharyya
May 10, 2002·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Panayiotis V BenosGary D Stormo
Oct 1, 1990·Journal of Biomolecular Structure & Dynamics·M J BlommersC W Hilbers
Jun 19, 2008·The Journal of Physical Chemistry. B·Daniel SvozilJirí Sponer
Jul 10, 2010·The Journal of Physical Chemistry. B·Clarisse G RicciPaulo A Netz

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