TY - GEN
T1 - Periodicity-dependent characteristics of ten unique dinucleotides in nucleosomal structures
AU - Yang, Xi
AU - Yan, Hong
PY - 2010
Y1 - 2010
N2 - The periodic occurrence of dinucleotides observed in nucleosomes has long been thought to be closely related to the sequence-dependent helical anisotropy of DNA sequences. We conduct a statistical analysis on the structural characteristics of the dinucleotides containing the 10.5 periodicity and on those without that periodicity, using all nucleosomal structures published in the PDB. By categorizing performances on the distribution of value occurrences frequency, averaged value, averaged net value and their respective standard deviations, we give a detailed description as to the deformation preferences correlated with the periodicity for the 10 unique types of dinucleotides and summarize the possible roles of the significant steps in how they facilitate DNA bending. The results show that for some dinucleotides the stereochemical characteristics are highly periodicity-dependent while for others the periodicity is less or not at all important for their conformations. © 2010 American Institute of Physics.
AB - The periodic occurrence of dinucleotides observed in nucleosomes has long been thought to be closely related to the sequence-dependent helical anisotropy of DNA sequences. We conduct a statistical analysis on the structural characteristics of the dinucleotides containing the 10.5 periodicity and on those without that periodicity, using all nucleosomal structures published in the PDB. By categorizing performances on the distribution of value occurrences frequency, averaged value, averaged net value and their respective standard deviations, we give a detailed description as to the deformation preferences correlated with the periodicity for the 10 unique types of dinucleotides and summarize the possible roles of the significant steps in how they facilitate DNA bending. The results show that for some dinucleotides the stereochemical characteristics are highly periodicity-dependent while for others the periodicity is less or not at all important for their conformations. © 2010 American Institute of Physics.
KW - Deformation preferences
KW - Dinucleotides
KW - DNA bending
KW - Flexibility
KW - Nuleosomes
KW - Periodicity-susceptibility
KW - Sequence-dependent helical anisotropy
UR - https://www.scopus.com/pages/publications/76749112524
UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-76749112524&origin=recordpage
U2 - 10.1063/1.3314270
DO - 10.1063/1.3314270
M3 - RGC 32 - Refereed conference paper (with host publication)
SN - 9780735407473
VL - 1210
SP - 57
EP - 68
BT - AIP Conference Proceedings
T2 - 2009 International Symposium on Computational Models for Life Sciences, CMLS 2009
Y2 - 28 July 2009 through 29 July 2009
ER -