Models Begin To Unravel How Single DNA Strands Combine

Using computer simulations, a team of University of
Wisconsin-Madison researchers has identified some of the pathways through
which single complementary strands of DNA interact and combine to form the
double helix.



Present in the cells of all living organisms, DNA is composed of two
intertwined strands and contains the genetic "blueprint" through which all
living organisms develop and function. Individual strands consist of
nucleotides, which include a base, a sugar and a phosphate moiety.



Understanding hybridization, the process through which single DNA strands
combine to form a double helix is fundamental to biology and central to
technologies such as DNA microchips or DNA-based nanoscale assembly. The
research by the Wisconsin group begins to unravel how DNA strands come
together and bind to each other, says Juan J. de Pablo, UW-Madison Howard
Curler Distinguished Professor of Chemical and Biological Engineering.



The team published its findings in the Proceedings of the
National Academy of Sciences. In addition to senior author de Pablo, the
group included David C. Schwartz, a UW-Madison professor of chemistry and
genetics, and former postdoctoral research fellow Edward J. Sambriski, now
an assistant professor of chemistry at Delaware Valley College in
Pennsylvania.



The three drew on detailed molecular DNA models developed by de Pablo's
research group to study the reaction pathways through which
double-stranded DNA undergo denaturation, where the molecule uncoils and
separates into single strands, and hybridization, through which
complementary DNA strands bind, or "hybridize." In Watson-Crick base
pairing, A (adenine) pairs with T (thymine), while G (guanine) pairs with
C (cytosine). Reaction pathways are the trajectories single DNA strands
follow to find each other and connect via such complementary pairs.



The researchers studied both random and repetitive base sequences. Random
sequences of the four bases - A, T, G and C - contained little or no
regular repetition. To the researchers' surprise, a couple of bases
located toward the center of the strand associate early in the
hybridization process. The moment they find each other, they bind and the
entire molecule hybridizes rapidly and in a highly organized manner.


Conversely, in repetitive sequences, the bases alternated regularly, and
the group found that these sequences bind through a so-called diffusive
process. "The two strands of DNA somehow find each other, they connect to
each other in no particular order, and then they slide past each other for
a long time until the exact complements find one another in the right
order, and then they hybridize," says de Pablo.



Results of the team's study show that DNA hybridization is very sensitive
to DNA composition, or sequence. "Contrary to what was thought previously,
we found that the actual process by which complementary DNA strands
hybridize is very sensitive to the sequence of the molecules," he says.



Knowledge of how the process occurs could enable researchers to more
strategically design technologies such as gene chips. For example, says de
Pablo, if a researcher wanted to design sequences that bind very rapidly
or with high efficiency, he or she could place certain bases in specific
locations, so that the hybridization reaction could occur faster or more
reliably.



Ultimately, the research could help biologists understand why some
hybridization reactions are faster or more robust than others. "One of the
really exciting things about this work is that the hybridization reaction
between two strands of DNA is really fundamental to life itself," says de
Pablo. "It is the basis for much of biology. And it is amazing to me that,
until now, we knew little of how this reaction actually proceeds."



The National Science Foundation-funded Nanoscale Science and Engineering
Center on Templated Synthesis and Assembly at the Nanoscale at UW-Madison
sponsored the research.




Source
University of Wisconsin-Madison