Large-Scale DNA Juxtaposition [Jian et al., 1998; Huang et al., 2001]

DNA supercoiling regulates many biological processes [Calladine & Drew, 1997; Cozzarelli & Wang, 1990; Vologodskii & Cozzarelli, 1994] that depend on torsional stress and the spatial approach of linearly distant DNA segments, as in transcription and site-specific recombination. Dynamic properties of supercoiling are barely understood, compounded by lack of experimental techniques. Therefore, computer simulations of DNA supercoiling can delineate mechanisms and hypotheses for testing.

Our studies of superhelical-DNA juxtaposition reported, for the first time, juxtaposition as a function of the superhelical density, DNA length, site separation [Jian et al., 1998], and the monovalent salt concentration [Huang et al., 2001]. Surprisingly, we showed qualitatively different kinetic mechanisms of juxtaposition as a function of salt: large-scale Brownian motion at low-to-moderate salt versus slithering (`reptation'), correlated with formation/deletion of branches, at high salt. Our subsequent hypothesis -- site juxtaposition may become rate-limiting for biochemical reactions requiring juxtaposition of 2 sites along DNAs >100 kb [Huang et al., 2001] -- might help design optimal conditions for site-specific recombination.

• Article -- "Dynamics of Site Juxtaposition in Supercoiled DNA"
  
  
• Article -- "Internal Motion of Supercoiled DNA: Brownian Dynamics Simulations of Site Juxtaposition"
  
  
• Article -- "A Combined Wormlike Chain and Bead Model for Dynamic Simulations of Long DNA"
  
  
• Article -- "Computer Simulations of Supercoiled DNA Energetics and Dynamics"
  
  
• Article -- "Trefoil Knotting Revealed by Molecular Dynamics of Supercoiled DNA"
  
  
• Article -- "On Higher Buckling Transition in Supercoiled DNA"
  
  
• Article -- "Beyond Optimization: Simulating the Dynamics of Supercoiled DNA by a Macroscopic Model"
  
  
• Article -- "Modeling Superhelical DNA: Recent Analytical and Dynamic Approaches"
  
  
• Article -- "Computational Challenges in Simulating Large DNA over Long Times"
  
  
• Art Gallery -- "Supercoiled DNA Dynamics "
  
  
• Jing Huang's Home Page
  
  

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