2024
JW Shepherd, S Guilbaud, Z Zhou, J Howard, M Burman, A Noy, and MC Leake (2024) “DNA plectoneme size, position, and mobility revealed by fluorescence microscopy and combined optical and magnetic tweezers” Nat Commun, 15, 2748 https://www.nature.com/articles/s41467-024-47126-6
T Gardasevic, A Noy (2024) “The impact of sequence periodicity on DNA
elasticity: the origin of A-tract’s curvature” Submitted
2023
M Burman and A Noy (2023) “Atomic description of the reciprocal action between supercoils and melting bubbles on linear DNA” Under Review. bioRxiv https://doi.org/10.1101/2023.06.21.545919
YAG Fosado, J Howard, A Noy, MC Leake, D Michieletto (2023) “Fluidification of entanglements by a DNA bending protein” Phy Rev Lett, 130, 058203, https://doi.org/10.1103/PhysRevLett.130.058203
2022
GD Watson, EW Chan, MC Leake, A Noy (2022) “Structural interplay between DNA-shape protein recognition and supercoiling: the case of IHF” Comput Struct Biotech J, 20, 5264-5274 https://doi.org/10.1016/j.csbj.2022.09.020
GD Watson, V Velasco-Berrelleza, A Noy (2022) “Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments” Meth Mol Biol, 2476, 95-109 https://link.springer.com/protocol/10.1007/978-1-0716-2221-6_8
EL Kristoffersen, M Burman, A Noy, P Holliger (2022) “Rolling Circle RNA Synthesis Catalysed by RNA” eLife, 11, e75186 https://elifesciences.org/articles/75186
2021
G da Rosa, L Grille, V Calzada, K Ahmad, JP Arcon, F Battistini, G Bayarri, T Bishop, P Carloni, T Cheatham III, R Collepardo-Guevara, J Czub, JR Espinosa, R Galindo-Murillo, SA Harris, A Hospital, C Laughton, JH Maddocks, A Noy, M Orozco, M Pasi, A Pérez, D Petkevičiūtė-Gerlach, R Sharma, R Sun, PD Dans (2021). “Sequence‑ dependent structural properties of B‑DNA: what have we learned in 40 years?” Biophys Rev
SB Yoshua, GD Watson, JAL Howard, V Velasco-Berrelleza, MC Leake, A Noy (2021). “Integration host factor bends and bridges DNA in multiplicity of binding modes with varying specificity ” Nuc Acids Res, 49,8684-8698 https://doi.org/10.1093/nar/gkab641
A Backer, G King, A Biebricher, JW Shepherd, A Noy, MC Leake, I Heller, GJL Wuite, E Peterman (2021). “Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA using Fluorescence Polarization Microscopy” J Phys Chem B, 125, 2351-2361 https://doi.org/10.1021/acs.jpcb.1c02708
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 (2021). “Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides” Nat Commun, 12, 1053 https://www.nature.com/articles/s41467-021-21243-y (shared first author and corresponding author)
2020
V Velasco-Berrelleza, M Burman, JW Shepherd, MC Leake, R Golestanian, A Noy (2020). “SerraNA: a program to determine nucleic acids elasticity from simulation data” Phys Chem Chem Phys, 22, 19254-19266 https://doi.org/10.1039/D0CP02713H
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)
Postdoc stage
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.2016.12.034. Highlighted 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
PhD stage
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
Agnes Noy 