Ludmil B Alexandrov1,2, Alan R Bishop3, Kim Ø Rasmussen4, Boian S Alexandrov5. 1. Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. lba@lanl.gov. 2. Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA. lba@lanl.gov. 3. Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. arb@lanl.gov. 4. Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. kor@lanl.gov. 5. Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA. boian@lanl.gov.
Abstract
BACKGROUND: The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this study, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization. RESULTS: We calculate the cyclization rates of 86 DNA sequences with previously measured J factors and lengths between 57 and 325 bp as well as of 20,000 randomly generated DNA sequences with lengths between 350 and 4000 bp. Our comparison with experimental data is complemented with analysis of simulated data. CONCLUSIONS: Our data demonstrate that all sets of parameters yield very similar results for longer DNA fragments, regardless of the nucleotide sequence, which are in agreement with experimental measurements. However, for DNA fragments shorter than 100 bp, all sets of parameters performed poorly yielding results with several orders of magnitude difference from the experimental measurements. Our data show that DNA cyclization rates calculated using conformational parameters based on nucleosome packaging data are most similar to the experimental measurements. Overall, our study provides a comprehensive large-scale assessment of the role of structural parameters in calculating DNA cyclization rates.
BACKGROUND: The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this study, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization. RESULTS: We calculate the cyclization rates of 86 DNA sequences with previously measured J factors and lengths between 57 and 325 bp as well as of 20,000 randomly generated DNA sequences with lengths between 350 and 4000 bp. Our comparison with experimental data is complemented with analysis of simulated data. CONCLUSIONS: Our data demonstrate that all sets of parameters yield very similar results for longer DNA fragments, regardless of the nucleotide sequence, which are in agreement with experimental measurements. However, for DNA fragments shorter than 100 bp, all sets of parameters performed poorly yielding results with several orders of magnitude difference from the experimental measurements. Our data show that DNA cyclization rates calculated using conformational parameters based on nucleosome packaging data are most similar to the experimental measurements. Overall, our study provides a comprehensive large-scale assessment of the role of structural parameters in calculating DNA cyclization rates.
Authors: Juan Wei; Luke Czapla; Michael A Grosner; David Swigon; Wilma K Olson Journal: Proc Natl Acad Sci U S A Date: 2014-11-10 Impact factor: 11.205