Publications

S Yoshua, G Watson, J Howard, V Velasco-Berrelleza, MC Leake, A Noy* (2020). “A nucleoid-associated protein bends and bridges DNA in a multiplicity of topological states with varying specificity” bioRxiv. https://doi.org/10.1101/2020.04.17.047076

V Velasco-Berrelleza, M Burmann, JW Shepherd, MC Leake, R Golestanian, A Noy* (2020). “SerraNA: a program to determine nucleic acids elasticity from simulation data” bioRxiv. https://doi.org/10.1101/2020.03.24.004945

ALB Pyne, A Noy*, K Main, V Velasco-Berrelleza, MM Piperakis, LA Mitchenall, FM Cugliandolo, JG Beton, CEM Stevenson, BW Hoogenboom, AD Bates, A Maxwell, SA Harris (2020). “Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and recognition” bioRxiv. https://doi.org/10.1101/863423 (shared first author and corresponding author)

ASB Jalal, NT Tran, CE Stevenson, EW Chan, RL, Xiao Tan, A Noy, DM Lawson, TBK Le (2020). “Diversification of DNA-binding specificity via permissive and specificity-switching mutations in the ParB/Noc protein family” Cell Reports, 32, 107928. https://doi.org/10.1016/j.celrep.2020.107928

JW Shepherd, RJ Greenall, MIJ Probert, A Noy*, MC Leake (2020). “The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA”. Nuc Acids Res, 48, 1748-63. https://doi.org/10.1093/nar/gkz1227 (corresponding auhtor)

A Noy, A Maxwell, SA Harris (2017). “Interference between triplex and protein binding to distal sites on supercoiled DNA” Biophys J, 112, 523-531. DOI: 10.1016/j.bpj.2016.12.034Highlighted article.

T Sutthibutpong, C Matek, CJ Benham, GG Slade, A Noy, C Laughton, JPK Doye, AA Louis and SA Harris (2016). “Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation” Nuc Acids Res,  44, 9121-9130. DOI: 10.1093/nar/gkw815

A Noy, T Sutthibutpong and SA Harris (2016). “Protein/DNA interactions in complex DNA topologies: expect the unexpected” Biophys Rev, 8, 233. DOI:10.1007/s12551-016-0208-8

T Sutthibutpong, A Noy and SA Harris (2016). “Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance and Analysis” Meth Mol Biol, 1431, 195. DOI 10.1007/978-1-4939-3631-1_15

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 (2016). “Parmbsc1: a refined force-field for DNA simulations” Nature Methods, 13, 55. DOI:10.1038/nmeth.3658

Sutthibutpong T, Harris SA, Noy A* (2015). “Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA” J Chem Theor Comput, 11, 2768. DOI:10.1021/acs.jctc.5b00035

Noy A, Golestanian R (2013). Comment on “Length scale dependence of DNA mechanical properties” Reply Phys Rev Lett, 111, 179802. DOI:10.1103/PhysRevLett.111.179802

Bates AD, Noy A, Piperakis MM, Harris SA, Maxwell A (2013). “Small DNA circles as a probes of DNA topology” Biochem Soc Trans, 41, 565-70. DOI: 10.1042/BST20120320

Noy A, Golestanian R (2012) “Length dependence of DNA mechanical properties” Phys Rev Lett, 109, 228101. DOI:10.1103/PhysRevLett.109.228101. Highlighted Article with the corresponding focus: Ball P. Physics 5, 134 (2012).

Noy A, Golestanian R (2010) “The chirality of DNA: elasticity cross-terms at base-pair level including A-tracts and the influence of ionic strength” J Phys Chem B, 114, 8022-31. DOI: 10.1021/jp104133j

Noy A, Soteras I, Luque FJ, Orozco M (2009). “The impact of monovalent ion force field model in nucleic acids simulations” Phys Chem Chem Phys, 11, 10596-607. DOI: 10.1039/B912067J

Orozco M, Noy A, Perez A (2008). “Recent Advances in the study of nucleic acid flexibility by molecular dynamics” Curr Opin Struct Biol, 18, 185-93. DOI:10.1016/j.sbi.2008.01.005

Noy A, Luque FJ, Orozco M (2008). “Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility” J Am Chen Soc, 130, 3486-96. DOI: 10.1021/ja076734u

Noy A, Perez A, Laughton CA, Orozco M (2007. “Theoretical study of large conformational transitions in DNA: the B-A conformational change in water and ethanol/water” Nuc Acids Res, 35, 3330-8. DOI: 10.1093/nar/gkl1135

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 (2006). “Data mining of molecular dynamics trajectories of nucleic acids” J Biomol Struct Dynam, 23, 447-56. DOI: 10.1080/07391102.2006.10507070

Noy A, Perez A, Marquez M, Luque FJ, Orozco M (2005). “Structure, recognition properties, and flexibility of the DNA.RNA hybrid” J Am Chem Soc, 127, 4910-20. DOI: 10.1021/ja043293v

Perez A, Noy A, Lankas F, Luque FJ, Orozco M (2004). “The relative flexibility of B-DNA and A-RNA duplexes: database analysis” Nuc Acids Res, 32, 6144-51. DOI: 10.1093/nar/gkh954

Noy A, Perez A, Lankas F, Luque FJ, Orozco M (2004). “Relative flexibility of DNA and RNA: a molecular dynamics study” J Mol Biol, 343, 627-38. DOI:10.1016/j.jmb.2004.07.048

Orozco M, Perez A, Noy A, Luque FJ (2003). “Theoretical methods for the simulation of nucleic acids” Chem Soc Rev, 32, 350-64. DOI: 10.1039/B207226M