Publications

2017
  1. A Noy, A Maxwell, SA Harris, “Interference between triplex and protein binding to distal sites on supercoiled DNA” Biophysics Journal, (2017), 112, 523-531. DOI: 10.1016/j.bpj.2016.12.034. Highlighted article.
2016
  1. T Sutthibutpong, C Matek, CJ Benham, GG Slade, A Noy, C Laughton, JPK Doye, AA Louis and SA Harris. “Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation” Nucleic Acids Research, (2016).  44, 9121-9130. DOI: 10.1093/nar/gkw815
  2. A Noy, T Sutthibutpong and SA Harris. “Protein/DNA interactions in complex DNA topologies: expect the unexpected” Biophysical Review, (2016), 8, 233. DOI:10.1007/s12551-016-0208-8
  3. T Sutthibutpong, A Noy and SA Harris. “Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance and Analysis” Meth Mol Biol, (2016), 1431, 195. DOI 10.1007/978-1-4939-3631-1_15
  4. Ivan II, Dans PD, Noy A, Perez A, Faustino I, Hopsital A, Walther J, Andrio P, Goni R, Balaceanu A, Portella G, Battistini F, Gelpi JL, Gomez-Pinto I, Gonzalez C, Vendruscolo M, Laughton CA, Harris SA, Case, Orozco M. “Parmbsc1: a refined force-field for DNA simulations” Nature Methods, (2016), 13, 55. DOI:10.1038/nmeth.3658
Older
  1. Sutthibutpong T, Harris SA, Noy A. “Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA” J Chem Theor Comput, (2015), 11, 2768. DOI:10.1021/acs.jctc.5b00035
  2. Noy A, Golestanian R. Comment on “Length scale dependence of DNA mechanical properties” Reply Phys Rev Lett, (2013), 111, 179802. DOI:10.1103/PhysRevLett.111.179802
  3. Bates AD, Noy A, Piperakis MM, Harris SA, Maxwell A. “Small DNA circles as a probes of DNA topology” Biochem Soc Trans, (2013), 41, 565-70. DOI: 10.1042/BST20120320
  4. Noy A, Golestanian R. “Length dependence of DNA mechanical properties” Phys Rev Lett, (2012), 109, 228101. DOI:10.1103/PhysRevLett.109.228101.
    Highlighted Article with the corresponding focus: Ball P. Physics 5, 134 (2012).
  5. Noy A, Golestanian R. “The chirality of DNA: elasticity cross-terms at base-pair level including A-tracts and the influence of ionic strength” J Phys Chem B, (2010), 114, 8022-31. DOI: 10.1021/jp104133j
  6. Noy A, Soteras I, Luque FJ, Orozco M. “The impact of monovalent ion force field model in nucleic acids simulations” Phys Chem Chem Phys, (2009), 11, 10596-607. DOI: 10.1039/B912067J
  7. Orozco M, Noy A, Perez A. “Recent Advances in the study of nucleic acid flexibility by molecular dynamics” Curr Opin Struct Biol, (2008), 18, 185-93. DOI:10.1016/j.sbi.2008.01.005
  8. Noy A, Luque FJ, Orozco M. “Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility” J Am Chen Soc, (2008), 130, 3486-96. DOI: 10.1021/ja076734u
  9. Noy A, Perez A, Laughton CA, Orozco M. “Theoretical study of large conformational transitions in DNA: the B-A conformational change in water and ethanol/water” Nuc Acids Res, (2007), 35, 3330-8. DOI: 10.1093/nar/gkl1135
  10. Noy A, Meyer T, Rueda M, Ferrer C, Valencia A, Prez A, de la Cruz X, Lopez-Bes JM, Pouplana R, Fernandez-Recio J, Luque FJ, Orozco M. “Data mining of molecular dynamics trajectories of nucleic acids” J Biomol Struct Dynam, (2006), 23, 447-56. DOI: 10.1080/07391102.2006.10507070
  11. Noy A, Perez A, Marquez M, Luque FJ, Orozco M. “Structure, recognition properties, and flexibility of the DNA.RNA hybrid” J Am Chem Soc, (2005), 127, 4910-20. DOI: 10.1021/ja043293v
  12. Perez A, Noy A, Lankas F, Luque FJ, Orozco M. “The relative flexibility of B-DNA and A-RNA duplexes: database analysis” Nuc Acids Res, (2004), 32, 6144-51. DOI: 10.1093/nar/gkh954
  13. Noy A, Perez A, Lankas F, Luque FJ, Orozco M. “Relative flexibility of DNA and RNA: a molecular dynamics study” J Mol Biol, (2004), 343, 627-38. DOI:10.1016/j.jmb.2004.07.048
  14. Orozco M, Perez A, Noy A, Luque FJ. “Theoretical methods for the simulation of nucleic acids” Chem Soc Rev, (2003), 32, 350-64. DOI: 10.1039/B207226M