Malaga Gadea, F.C. and Nikolova, E.N. Structural plasticity of pioneer factor Sox2 and DNA bendability modulate nucleosome engagement and Sox2-Oct4 synergism. J Mol Biol. 2023; 435(2):167916.
Nikolova, E.N., Stanfield, R., Dyson, H.J., Wright, P.E. A conformational switch in the zinc finger protein Kaiso mediates differential readout of specific and methylated DNA sequences Biochemistry. 2020; 59(20):1909-1926.
Nikolova, E.N., Stanfield, R., Dyson, H.J., Wright, P.E. CH---O hydrogen bonds mediate highly specific recognition of methylated CpG sites by the zinc finger protein Kaiso Biochemistry. 2018; 57(14):2109-2120.
Zhou H., Kimsey, I.J., Nikolova, E.N., Sathyamoorthy, B., Grazioli, G., McSally, J., Bai, T., Wunderlich, C.H., Andricioaei, I., Al-Hashimi, H.M. m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs Nat Struct Mol Biol. 2016; 23(9):803-10.
Salmon, L., Giambaşu, G.M., Nikolova, E.N., Petzold, K., Bhattacharya, A., Case, D.A., Al-Hashimi, H.M. Modulating RNA alignment using directional dynamic kinks: application in determining an atomic-resolution ensemble for a hairpin using NMR residual dipolar couplings. J Am Chem Soc. 2015; 137(40), 12954-65.
Nikolova, E.N., Stull, F., and Al-Hashimi, H.M. Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair Biochemistry 2014; 53(46), 7145-7.
Alvey, H.S., Gottardo, F.L., Nikolova, E.N., and Al-Hashimi, H.M. Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics Nat Commun. 2014; 5-4786.
Nikolova, E.N., Zhou, H., Gottardo, F.L., Alvey, H.S., Kimsey, I.J., Al-Hashimi, H.M. A historical account of Hoogsteen base-pairs in duplex DNA Biopolymers 2013; 99(12), 955-68.
Nikolova, E.N., Goh, G.B., Brooks, C.L. 3rd, and Al-Hashimi, H.M. Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA J Am Chem Soc. 2013; 135(18), 6766-9.
Nikolova, E.N., Bascom, G., Andricioaei, I., and Al-Hashimi, H.M. Probing sequence-specific DNA flexibility in A-tracts and pyrimidine-purine steps by NMR 13C relaxation and MD simulations Biochemistry 2012; 51(43), 8654-64.
Prevette, L., Nikolova, E.N., Al-Hashimi, H.M., and Banaszak Holl, M. Intrinsic dynamics of DNA-polymer complexes: a mechanism for DNA release Mol Pharm. 2012; 9(9), 2743-9.
Nikolova, E.N., Gottardo, F.L., and Al-Hashimi, H.M. Probing transient Hoogsteen hydrogen bonds in canonical duplex DNA using NMR relaxation dispersion and single-atom substitution J Am Chem Soc. 2012; 134(8), 3667-70.
Bothe, J.R., Nikolova, E.N., Eichhorn, C.D., Chugh, J., Hansen, A.L., and Al-Hashimi, H.M. Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy Nat Methods, 2011; 8(11):919-31.
Nikolova, E.N., Kim, E., Wise, A.A., O’Brien P., Andricioaei, I., and Al-Hashimi, H.M. Transient Hoogsteen base pairs in canonical duplex DNA Nature, 2011; 470(7335), 498.
Nikolova, E.N. and Al-Hashimi, H.M. Thermodynamics of RNA melting, one base pair at a time RNA, 2010; 16(9):1687.
Nikolova, E.N. and Al-Hashimi, H.M. Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR J Biomol NMR, 2009; 45(1-2), 9.
Hansen, A.L., Nikolova, E.N., Casiano-Negroni, A., and Al-Hashimi, H.M. Extending the range of microsecond-to-millisecond chemical exchange detected in labeled and unlabeled nucleic acids by selective carbon R(1rho) NMR spectroscopy J Am Chem Soc. 2009; 131, 3818.
Pereira, M.J.B., Nikolova, E.N., Hiley, S.L., Jaikaran, D., Collins, R.A. and Walter, N.G. Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis J Mol Biol. 2008; 382, 496.