Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs.

ABSTRACT:

Background

An important question of biological relevance is the polymorphism of the double-helical DNA structure in its free form, and the changes that it undergoes upon protein-binding. We have analysed a database of free DNA crystal structures to assess the inherent variability of the free DNA structure and have compared it with a database of protein-bound DNA crystal structures to ascertain the protein-induced variations.

Results

Most of the dinucleotide steps in free DNA display high flexibility, assuming different conformations in a sequence-dependent fashion. With the exception of the AA/TT and GA/TC steps, which are 'A-phobic', and the GG/CC step, which is 'A-philic', the dinucleotide steps show no preference for A or B forms of DNA. Protein-bound DNA adopts the B-con

SUBMITTER: Marathe A 

PROVIDER: S-EPMC2687451 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature