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Is hairpin formation in single-stranded polynucleotide diffusion-controlled?
Anjum Ansari1, Serguei V Kuznetsov
1Department of Physics and Department of Bioengineering, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, USA. ansari@uic.edu
The Journal of Physical Chemistry. B
|July 21, 2006
Summary
Biopolymer hairpin formation kinetics are slower than predicted. This study reveals that DNA and RNA hairpin dynamics are diffusion-controlled, influenced by solvent viscosity, impacting their formation rates.
Area of Science:
- Biopolymer science
- Molecular dynamics
- Physical chemistry
Background:
- Single-stranded DNA and RNA oligomers form hairpin structures on unexpectedly slow timescales.
- The slow kinetics suggest factors beyond simple loop formation influence hairpin dynamics.
Purpose of the Study:
- To investigate the origin of slow hairpin formation kinetics.
- To determine if hairpin dynamics are diffusion-controlled by examining the effect of solvent viscosity.
Main Methods:
- Laser temperature-jump techniques were employed to study hairpin kinetics.
- Solvent viscosity was altered by adding glycerol, a known hairpin destabilizer.
- Isostability conditions were established by adjusting temperature to isolate viscosity effects.
Main Results:
- Glycerol addition destabilized hairpins, complicating previous viscosity dependence studies.
- Under isostability conditions, both hairpin opening and closing times scaled with viscosity (approximately eta(1.1+/-0.1)).
- Previous studies reported erroneous scaling exponents due to uncorrected stability changes.
Conclusions:
- Hairpin dynamics are significantly coupled to solvent viscosity.
- The rate-determining step in hairpin formation involves the diffusion of the polynucleotide chain through the solvent.