Probability of the Site Juxtaposition Determines the Rate of Protein-Mediated DNA Looping
Yury S Polikanov 1, Vladimir A Bondarenko 1, Vladimir Tchernaenko 2, Yong I Jiang 3, Leonard Lutter 2, Alexander Vologodskii 4* and Vasily Studitsky 1
1 Robert Wood Johnson Medical School
2 Henry Ford Hospital
3 Cleveland Clinic Foundation
4 New York University
* To whom correspondence should be addressed. E-mail: alex.vologodskii{at}nyu.edu.
Submitted on April 23, 2007
Revised on May 10, 2007
Accepted on 13 June 2007
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Abstract |
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Numerous biological processes are regulated by DNA elements that communicate with their targets over a distance, via formation of protein-bridged DNA loops. One of the first questions arising in studies of DNA looping is whether the rate of loop formation is limited by diffusion of the DNA sites. We addressed this question by comparing the in vitro measured rates of transcription initiation in the NtrC-glnAp2 enhancer-dependent transcription initiation system with predictions of two different theoretical models. The promoter and enhancer were in 7.6 kb plasmid and separated by 2.5 kb. The measurements were performed for different values of the plasmid superhelix density, from 0 till -0.07. Earlier theoretical analysis, based on the Monte Carlo simulation of DNA conformations, showed that if the rate of the loop formation is determined by the equilibrium probability of juxtaposition of the DNA sites, the rate should be approximately hundred times higher in supercoiled DNA than in relaxed one. On the other hand, Brownian dynamics simulation showed that if the rate of loop formation is limited by the site diffusion, it should be nearly independent on DNA supercoiling. We found that efficiency of the transcription initiation increases by nearly two orders of magnitude due to the corresponding increase of the template supercoiling. This clearly shows that the rate of bridging in the enhancer-promoter system is not limited by diffusion of the DNA sites one to another. We argue that this conclusion derived for the specific system is likely to be valid for the great majority of biological processes involving protein-mediated DNA looping.
Key Words:
DNA loop formation, DNA supercoiling, Diffusion-limited process, Enhancer-promoter interaction, RNA polymerase
