Evgenia Nikolova

Evgenia Nikolova

Assistant Research Professor

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Biophysics > People > Evgenia Nikolova

Dr. Evgenia Nikolova obtained her undergraduate degree from Lafayette College and completed her graduate studies with Professor Hashim Al-Hashimi at the University of Michigan. At the Al-Hashimi lab, she investigated the structure and dynamics of nucleic acids using nuclear magnetic resonance (NMR) spectroscopy and computational approaches and discovered the presence of alternative transient base pairs in DNA duplexes.

Evgenia continued her postdoctoral training with Professor Peter Wright at the Scripps Research Institute (La Jolla), where she studied the DNA binding properties of zinc finger transcriptional factors using NMR, crystallography, and biochemistry to elucidate how they discriminate between specific and methylated nucleotide sequences. In 2017, she joined the Biophysics Department at Johns Hopkins and has since been pursuing research into how regulatory proteins interact with chromatin and change its structure and dynamics.

Evgenia is broadly interested in studying the structure and dynamics of nucleic acids and their protein complexes and how those relate to biological function. Research in her lab is currently focused on looking at the interaction of nucleosomes (basic units of chromatin packaging) with regulatory proteins named “pioneer factors”. These are transcription factors that have the unique ability to engage their DNA target sites in highly condensed and transcriptionally silent regions of chromatin and, with the help of other proteins, locally open chromatin and activate gene expression. Pioneer factors play critical roles in development and differentiation, yet it remains unclear at the molecular level how they find their binding sites and change the structure and transcriptional state of chromatin. Evgenia's lab is trying to address these gaps in mechanistic knowledge by using a spectrum of biochemical and biophysical experiments as well as by developing novel technologies.

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.