Search Results - "Nikolova, Evgenia N"

Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy by Bothe, Jameson R, Nikolova, Evgenia N, Eichhorn, Catherine D, Chugh, Jeetender, Hansen, Alexandar L, Al-Hashimi, Hashim M

“…In this Review, the authors thoroughly discuss solution-state NMR spectroscopy methods used for characterizing the dynamic structure landscape of RNA…”
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A historical account of hoogsteen base-pairs in duplex DNA by Nikolova, Evgenia N., Zhou, Huiqing, Gottardo, Federico L., Alvey, Heidi S., Kimsey, Isaac J., Al-Hashimi, Hashim M.

“…ABSTRACT In 1957, a unique pattern of hydrogen bonding between N3 and O4 on uracil and N7 and N6 on adenine was proposed to explain how poly(rU) strands can…”
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Characterizing the Protonation State of Cytosine in Transient G·C Hoogsteen Base Pairs in Duplex DNA by Nikolova, Evgenia N, Goh, Garrett B, Brooks, Charles L, Al-Hashimi, Hashim M

“…G·C Hoogsteen base pairs can form transiently in duplex DNA and play important roles in DNA recognition, replication, and repair. G·C Hoogsteen base pairs are…”
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Probing Sequence-Specific DNA Flexibility in A‑Tracts and Pyrimidine-Purine Steps by Nuclear Magnetic Resonance 13C Relaxation and Molecular Dynamics Simulations by Nikolova, Evgenia N, Bascom, Gavin D, Andricioaei, Ioan, Al-Hashimi, Hashim M

“…Sequence-specific DNA flexibility plays a key role in a variety of cellular interactions that are critical for gene packaging, expression, and regulation, yet…”
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Structural Plasticity of Pioneer Factor Sox2 and DNA Bendability Modulate Nucleosome Engagement and Sox2-Oct4 Synergism by Malaga Gadea, Fabiana C., Nikolova, Evgenia N.

“…[Display omitted] •Pioneer factors Sox2 and Oct4 bind compacted chromatin and promote transcription.•Strong Sox2-nucleosome binding at SHL5 mimics the folded…”
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Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics by Alvey, Heidi S., Gottardo, Federico L., Nikolova, Evgenia N., Al-Hashimi, Hashim M.

“…Hoogsteen (HG) base pairing involves a 180° rotation of the purine base relative to Watson–Crick (WC) base pairing within DNA duplexes, creating alternative…”
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m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs by Zhou, Huiqing, Kimsey, Isaac J, Nikolova, Evgenia N, Sathyamoorthy, Bharathwaj, Grazioli, Gianmarc, McSally, James, Bai, Tianyu, Wunderlich, Christoph H, Kreutz, Christoph, Andricioaei, Ioan, Al-Hashimi, Hashim M

“…The B-DNA double helix can dynamically accommodate G-C and A-T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G-C(+) (in…”
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A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences by Nikolova, Evgenia N, Stanfield, Robyn L, Dyson, H. Jane, Wright, Peter E

“…Recognition of the epigenetic mark 5-methylcytosine (mC) at CpG sites in DNA has emerged as a novel function of many eukaryotic transcription factors (TFs). It…”
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CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso by Nikolova, Evgenia N, Stanfield, Robyn L, Dyson, H. Jane, Wright, Peter E

“…Many eukaryotic transcription factors recognize the epigenetic marker 5-methylcytosine (mC) at CpG sites in DNA. Despite their structural diversity,…”
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Extending the range of microsecond-to-millisecond chemical exchange detected in labeled and unlabeled nucleic acids by selective carbon R(1rho) NMR spectroscopy by Hansen, Alexandar L, Nikolova, Evgenia N, Casiano-Negroni, Anette, Al-Hashimi, Hashim M

“…We present an off-resonance carbon R(1rho) NMR experiment utilizing weak radiofrequency fields and selective polarization transfers for quantifying…”
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Extending the Range of Microsecond-to-Millisecond Chemical Exchange Detected in Labeled and Unlabeled Nucleic Acids by Selective Carbon R1ρ NMR Spectroscopy by Hansen, Alexandar L, Nikolova, Evgenia N, Casiano-Negroni, Anette, Al-Hashimi, Hashim M

“…We present an off-resonance carbon R1ρ NMR experiment utilizing weak radiofrequency fields and selective polarization transfers for quantifying…”
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Guanine to Inosine Substitution Leads to Large Increases in the Population of a Transient G.C Hoogsteen Base Pair by Nikolova, Evgenia N, Stull, Frederick, Al-Hashimi, Hashim M

“…We recently showed that Watson-Crick base pairs in canonical duplex DNA exist in dynamic equilibrium with G(syn).C super(+) and A(syn).T Hoogsteen base pairs…”
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Guanine to Inosine Substitution Leads to Large Increases in the Population of a Transient G·C Hoogsteen Base Pair by Nikolova, Evgenia N, Stull, Frederick, Al-Hashimi, Hashim M

“…We recently showed that Watson–Crick base pairs in canonical duplex DNA exist in dynamic equilibrium with G­(syn)·C+ and A­(syn)·T Hoogsteen base pairs that…”
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Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations by Nikolova, Evgenia N, Bascom, Gavin D, Andricioaei, Ioan, Al-Hashimi, Hashim M

“…Sequence-specific DNA flexibility plays a key role in a variety of cellular interactions that are critical for gene packaging, expression, and regulation, yet…”
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Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings by Salmon, Loïc, Giambaşu, George M, Nikolova, Evgenia N, Petzold, Katja, Bhattacharya, Akash, Case, David A, Al-Hashimi, Hashim M

“…Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the…”
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Transient Hoogsteen base pairs in canonical duplex DNA by Nikolova, Evgenia N., Kim, Eunae, Wise, Abigail A., O’Brien, Patrick J., Andricioaei, Ioan, Al-Hashimi, Hashim M.

“…Sequence-directed variations in the canonical DNA double helix structure that retain Watson–Crick base-pairing have important roles in DNA recognition,…”
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Probing Transient Hoogsteen Hydrogen Bonds in Canonical Duplex DNA Using NMR Relaxation Dispersion and Single-Atom Substitution by Nikolova, Evgenia N, Gottardo, Federico L, Al-Hashimi, Hashim M

“…Nucleic acids transiently morph into alternative conformations that can be difficult to characterize at the atomic level by conventional methods because they…”
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Thermodynamics of RNA melting, one base pair at a time by Nikolova, Evgenia N, Al-Hashimi, Hashim M

“…The melting of base pairs is a ubiquitous feature of RNA structural transitions, which are widely used to sense and respond to cellular stimuli. A recent study…”
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Intrinsic Dynamics of DNA–Polymer Complexes: A Mechanism for DNA Release by Prevette, Lisa E, Nikolova, Evgenia N, Al-Hashimi, Hashim M, Banaszak Holl, Mark M

“…The transfer of genetic material into cells using nonviral vectors offers unique potential for therapeutics; however, the efficacy of delivery depends upon a…”
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Preparation, resonance assignment, and preliminary dynamics characterization of residue specific ¹³C/¹⁵N-labeled elongated DNA for the study of sequence-directed dynamics by NMR by Nikolova, Evgenia N, Al-Hashimi, Hashim M

“…DNA is a highly flexible molecule that undergoes functionally important structural transitions in response to external cellular stimuli. Atomic level spin…”
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