Další formáty:
BibTeX
LaTeX
RIS
@article{1202574, author = {Drsata, Tomáš and Špačková, Naďa and Jurečka, Petr and Zgarbová, Marie and Šponer, Jiří and Lankaš, Filip}, article_location = {Oxford}, article_number = {11}, doi = {http://dx.doi.org/10.1093/nar/gku338}, keywords = {MOLECULAR-DYNAMICS SIMULATIONS; SEQUENCE-DIRECTED CURVATURE; ADENINE-THYMINE TRACT; BASE-PAIR LEVEL; INDIRECT READOUT; NUCLEIC-ACIDS; B-DNA; CONFORMATIONAL-ANALYSIS; DISFAVORING SEQUENCES; ELASTIC PROPERTIES}, language = {eng}, issn = {0305-1048}, journal = {Nucleic Acids Research}, title = {Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning}, url = {http://nar.oxfordjournals.org/content/early/2014/05/29/nar.gku338}, volume = {42}, year = {2014} }
TY - JOUR ID - 1202574 AU - Drsata, Tomáš - Špačková, Naďa - Jurečka, Petr - Zgarbová, Marie - Šponer, Jiří - Lankaš, Filip PY - 2014 TI - Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning JF - Nucleic Acids Research VL - 42 IS - 11 SP - 7383-7394 EP - 7383-7394 PB - Oxford University Press SN - 03051048 KW - MOLECULAR-DYNAMICS SIMULATIONS KW - SEQUENCE-DIRECTED CURVATURE KW - ADENINE-THYMINE TRACT KW - BASE-PAIR LEVEL KW - INDIRECT READOUT KW - NUCLEIC-ACIDS KW - B-DNA KW - CONFORMATIONAL-ANALYSIS KW - DISFAVORING SEQUENCES KW - ELASTIC PROPERTIES UR - http://nar.oxfordjournals.org/content/early/2014/05/29/nar.gku338 L2 - http://nar.oxfordjournals.org/content/early/2014/05/29/nar.gku338 N2 - A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric A(n)T(n) and asymmetric A(2n) tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulations. We find that asymmetric A-tracts are more rigid than the control G/C-rich sequence in localized distortions relevant for nucleosome formation, but are more flexible in global bending and twisting relevant for looping. The symmetric tracts, in contrast, are more rigid than asymmetric tracts and the control, both locally and globally. Our results can reconcile the contradictory stiffness data on A-tracts and suggest symmetric A-tracts to be more efficient in nucleosome exclusion than the asymmetric ones. This would open a new possibility of gene expression manipulation using A-tracts. ER -
DRSATA, Tomáš, Naďa ŠPAČKOVÁ, Petr JUREČKA, Marie ZGARBOVÁ, Jiří ŠPONER a Filip LANKAŠ. Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2014, roč.~42, č.~11, s.~7383-7394. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gku338.
|