We are proud to announce the publication of this paper in the journal Nucleic Acids Research.

Abstract

We present a systematic study of the long-timescale dynamics of the Drew–Dickerson dodecamer (DDD: d(CGCGAATTGCGC)2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na+Cl− or K+Cl−. The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 μs) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 μs of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.

Authors

  1. Pablo D. Dans
  2. Linda Danilāne
  3. Ivan Ivani
  4. Tomáš Dršata
  5. Filip Lankaš
  6. Adam Hospital
  7. Jürgen Walther
  8. Ricard Illa Pujagut
  9. Federica Battistini
  10. Josep Lluis Gelpí
  11. Richard Lavery
  12. Modesto Orozco

Citation

Computational Biology:

Pablo D. Dans, Linda Danilāne, Ivan Ivani, Tomáš Dršata, Filip Lankaš, Adam Hospital, Jürgen Walther, Ricard Illa Pujagut, Federica Battistini,Josep Lluis Gelpí, Richard Lavery, and Modesto Orozco

Long-timescale dynamics of the Drew–Dickerson dodecamer Nucl. Acids Res. first published online April 15, 2016 doi:10.1093/nar/gkw264

Full Paper

http://nar.oxfordjournals.org/content/44/9/4052