|
rdf:type |
|
|
lifeskim:mentions |
|
|
pubmed:issue |
6
|
|
pubmed:dateCreated |
1998-2-5
|
|
pubmed:abstractText |
A combination of conformational search, energy minimization, and energetic evaluation using a continuum solvent treatment has been employed to study the stability of various conformations of the DNA fragment d(CGCAGAA)/d(TTCGCG) containing a single adenine bulge. The extra-helical (looped-out) bulge conformation derived from a published x-ray structure and intra-helical (stacked bulge base) model structures partially based on nuclear magnetic resonance (NMR) data were used as start structures for the conformational search. Solvent-dependent contributions to the stability of the conformations were calculated from the solvent exposed molecular surface area and by using the finite difference Poisson-Boltzmann approach. Three classes (I-III) of bulge conformations with calculated low energies can be distinguished. The lowest-energy conformations were found in class I, corresponding to structures with the bulge base stacked between flanking helices, and class II, composed of structures forming a triplet of the bulge base and a flanking base pair. All extra-helical bulge structures, forming class III, were found to be less stable compared with the lowest energy structures of class I and II. The results are consistent with NMR data on an adenine bulge in the same sequence context indicating an intra-helical or triplet bulge conformation in solution. Although the total energies and total electrostatic energies of the low-energy conformations show only relatively modest variations, the energetic contributions to the stability were found to vary significantly among the classes of bulge structures. All intra-helical bulge structures are stabilized by a more favorable Coulomb charge-charge interaction but destabilized by a larger electrostatic reaction field contribution compared with all extra-helical and most triplet bulge structures. Van der Waals packing interactions and nonpolar surface-area-dependent contributions appear to favor triplet class II structures and to a lesser degree also the intra-helical stacked bulge conformations. The large conformational variation found for class III conformers might add a favorable entropic contribution to the stability of the extra-helical bulge form.
|
|
pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-1477279,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-1507226,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-1593627,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-1621097,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-1637989,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-1991115,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2295611,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2300191,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2361138,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2482765,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2557907,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2619933,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2706253,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2730946,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2740330,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2742988,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2765499,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-2780311,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-3271421,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-3271422,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-3327519,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-3368313,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-3386751,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-3386752,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-3387215,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-3390425,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-3567151,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-3801425,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-7066296,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-7512653,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-7526401,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-7536250,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-7563057,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-7563092,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-7597079,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-7694230,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-7753866,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-7795634,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-8158653,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-8159662,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-8176736,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-8534822,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-8534823,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-8573566,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-8683589,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-8807843,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-8918800,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-9017183,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-9096232,
http://linkedlifedata.com/resource/pubmed/commentcorrection/9414214-9199796
|
|
pubmed:language |
eng
|
|
pubmed:journal |
|
|
pubmed:citationSubset |
IM
|
|
pubmed:chemical |
|
|
pubmed:status |
MEDLINE
|
|
pubmed:month |
Dec
|
|
pubmed:issn |
0006-3495
|
|
pubmed:author |
|
|
pubmed:issnType |
Print
|
|
pubmed:volume |
73
|
|
pubmed:owner |
NLM
|
|
pubmed:authorsComplete |
Y
|
|
pubmed:pagination |
2990-3003
|
|
pubmed:dateRevised |
2009-11-18
|
|
pubmed:meshHeading |
pubmed-meshheading:9414214-Adenine,
pubmed-meshheading:9414214-Algorithms,
pubmed-meshheading:9414214-Biophysical Phenomena,
pubmed-meshheading:9414214-Biophysics,
pubmed-meshheading:9414214-DNA,
pubmed-meshheading:9414214-Ions,
pubmed-meshheading:9414214-Magnetic Resonance Spectroscopy,
pubmed-meshheading:9414214-Models, Molecular,
pubmed-meshheading:9414214-Nucleic Acid Conformation,
pubmed-meshheading:9414214-Oligodeoxyribonucleotides,
pubmed-meshheading:9414214-Solvents,
pubmed-meshheading:9414214-Static Electricity,
pubmed-meshheading:9414214-Thermodynamics,
pubmed-meshheading:9414214-X-Ray Diffraction
|
|
pubmed:year |
1997
|
|
pubmed:articleTitle |
Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions.
|
|
pubmed:affiliation |
Max Delbrück Center for Molecular Medicine, Humboldt Universität Berlin, Institut für Biologie, Germany. martin@iris2.biosim.mdc-berlin.de
|
|
pubmed:publicationType |
Journal Article
|
