Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Influence of Global DNA Topology on Local Structured Transitions

Supercoiling is a fundamental structural feature of DNA that plays an important role in many genetic processes such as transcription, replication and recombination. Supercoiling allows distant DNA regions to be brought into close proximity. Little is known about possible effects of global DNA topology on the formation and stability of local structures. Positioned diametrically opposite in a circular molecule, two structural elements, which prefer an apical position, may be favored. This may result in a higher propensity of one or both structures to form. Alternatively, the circular molecule should adopt a Y-shape geometry (branched global structure) to provide an extra apical position to accommodate both structures. Thus, we tested the hypothesis that the topographic positioning of a sequence in a supercoiled molecule can influence its ability to undergo structural transitions. We created a series of plasmids containing an inverted repeat and an A-tract bent DNA sequence. A-tract forms a permanent 180° bend irrespective of DNA topology. The inverted repeat and the bent sequence were placed either at 6 o?clock or 3 o?clock positions with respect to each other. Using two-dimensional agarose gel electrophoresis, we show that the 6 o?clock construct extrudes the cruciform at a lower superhelical density than a control plasmid without the bend. Atomic force microscopy also shows that the 3 o?clock construct has the propensity to form branched molecules with two short arms with the cruciform at the end of one branch.

E. A. Oussatcheva1
V. N. Potaman1,*
J. Pavlicek3
Y. L. Lyubchenko2,3
L. S. Shlyakhtenko3
R. R. Sinden1

1Institute of Biosciences and Technology
Texas A&M University Health Sciences Center
2121 W. Holcombe Blvd.
Houston, TX 77030
Department of
Arizona State University
Tempe, AZ 85287
*Phone: (713) 677-7675
Fax: (713) 677-7689