Excluded volume effect in unzipping DNA with a force

✍ Scribed by Pui-Man Lam; J.C.S. Levy; Hanchen Huang

• Publisher: Wiley (John Wiley & Sons)
• Year: 2004
• Tongue: English
• Weight: 116 KB
• Volume: 73
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.10584

✦ Synopsis

Abstract

A double stranded DNA molecule when pulled with a force acting on one end of the molecule can become either partially or completely unzipped depending on the magnitude of the force F. For a random DNA sequence, the number M of unzipped base pairs goes as M≈(F − F~c~)^−2^ and diverges at the critical force F~c~ with an exponent χ = 2. We find that when excluded volume effect is taken into account for the unzipped part of the DNA, the exponent χ = 2 is not changed but the critical force F~c~ is changed. The force versus temperature phase diagram depends on only two parameters in the model, the persistence length and the denaturation temperature. Furthermore a scaling form of the phase diagram can be found. This scaling form is parameter independent and depends only on the spatial dimension. It applies to all DNA molecules and should provide a useful framework for comparison with experiments. © 2004 Wiley Periodicals, Inc. Biopolymers 73: 293–300, 2004