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Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing <i>versus </i>base sequence

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Title Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing versus base sequence
 
Creator Ghosh, Anirban
Bansal, Manju
 
Description 7-15
We have analyzed the set of inter and
intra base pair parameters for each dinucleotide step in single crystal
structures of dodecamers, solved at high and medium resolution and all
crystallized in P212121 space group. The
objective was to identify whether all the structures which have either the
Drew-Dickerson (DD) sequence d[CGCGAA TTCGCG) with some base modification or
related sequence (non-DO), would display the same sequence dependent structural
variability about its palindromic sequence, despite the molecule being bent at
one end because of similar crystal lattice packing effect. Most of the local
doublet parameters for base pairs steps G2-C3 and G 10-C 11 positions,
symmetrically situated about the lateral twofold, were significantly correlated
between themselves. In non-DD sequences, significant correlations between these
positional parameters were absent. The different range of local step parameter
values at each sequence position contributed to the gross feature of smooth
helix axis bending in all structures. The base pair parameters in some of the
positions, for medium resolution DD sequence, were quite unlike the
high-resolution set and encompassed a higher range of values. Twist and slide
are the two main parameters that show wider conformational range for the middle
region of non-DO sequence structures in comparison to DD sequence structures.
On the contrary, the minor and major groove features bear good resemblance
between DD and non-DD sequence crystal structure datasets. The sugar-phosphate
backbone torsion angles are similar in all structures, in sharp contrast to
base pair parameter variation for high and low resolution DD and non-DD
sequence structures, consisting of unusual (ε=g-, ξ=t) BII
conformation at the 10th position of the dodecamer sequence. Thus
examining DD and non-DD sequence structures packed in the same crystal lattice
arrangement, we infer that inter and intra base pair parameters are as
symmetrically equivalent in its value as the symmetry related step for the
palindromic DD sequence

about lateral two-fold axis. This feature
would lead us to agree with the conclusion that DNA conformation is not
substantially affected by end-to-end or lateral inter-molecular interaction due
to crystal lattice packing effect. Non-DD sequence structures acquire step
parameter values which reflect the altered sequence at each of the dodecamer
sequence position

in the orthorhombic lattice while showing
similar gross features of DD sequence structures.
 
Date 2013-07-16T05:19:48Z
2013-07-16T05:19:48Z
2001-04
 
Type Article
 
Identifier 0975-0959 (Online); 0301-1208 (Print)
http://hdl.handle.net/123456789/19791
 
Language en_US
 
Rights CC Attribution-Noncommercial-No Derivative Works 2.5 India
 
Publisher NISCAIR-CSIR, India
 
Source IJBB Vol.38(1-2) [February-April 2001]