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Title: Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA

We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction ε{sub hb}(AT) for an AT base pair and the ring factor ξ turn out to be the most sensitive parameters. In addition, the stacking interaction ε{sub st}(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased waymore » of optimization.« less
Authors:
; ;  [1] ; ;  [2] ;  [3]
  1. Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009 (India)
  2. Department of Chemistry, Bose Institute, 93/1 A P C Road, Kolkata 700 009 (India)
  3. Institute for Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany and Physics Department, Tampere University of Technology, FI-33101 Tampere (Finland)
Publication Date:
OSTI Identifier:
22253375
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 140; Journal Issue: 12; Other Information: (c) 2014 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 60 APPLIED LIFE SCIENCES; DNA; INTERACTIONS; REACTION KINETICS; SENSITIVITY ANALYSIS