Code word design for DNA computing with consideration of hybridization kinetics

Abstract:
Further understanding of DNA hybridization kinetics has new
urgency because recent DNA network systems often depends critically on
hybridization rates particularly under isothermal conditions. Indeed,
sequence-dependent decrease of performance for hybridization-based
oligonucleotide networks has been reported, and the mechanism is still
not understood. For this urgency, we have investigated quantitatively
the influence of secondary structures on the hybridization kinetics.
    I will present stopped-flow and microarray experiments for over a
hundred of DNA sequences' hybridization. These measurements clearly
indicate that fleeting single-stranded DNA secondary structures
suppress the hybridization kinetics. The fleeting secondary structures
that are less stable than unstructured, or random coil, have been
largely ignored in hybridization kinetics. Our findings provide a
novel factor for controlling the kinetics of nucleic acid reactions
and will be especially useful in the rational design of versatile DNA
and RNA nanodevices.

About the speaker:
Hiroaki Hata is a PhD student in physics at the University
of Tokyo. He belongs to Akira Suyama’s group and they have tried to
experimentally engineer smart molecular systems using biomolecules
like synthetic DNA. His research interest includes dynamic DNA
nanotechnology.