N.B. Ulyanov, selected publications

Cash D.D., Cohen-Zontag O., Kim N.K., Shefer K., Brown Y., Ulyanov N.B., Tzfati Y. & Feigon J. Pyrimidine motif triple helix in the Kluyveromyces lactis telomerase RNA pseudoknot is essential for function in vivo. Proc. Natl Acad. Sci. U.S.A. 110, 10970-75 (2013).

Ulyanov N.B. & James T.L. RNA structural motifs that entail hyndrogen bonds involving sugar-phosphate backbone atoms of RNA. New J. Chem. 34, 910-17 (2010).

Chung J, Ulyanov N.B., Guilbert C., Mujeeb C. & James T.L. Binding characteristics of small molecules that mimic nucleocapsid protein-induced maturation of stem-loop 1 of HIV-1 RNA. Biochemistry 49, 6341-51 (2010).

Wang D., Ulyanov N.B. & Zhurkin V.B. Sequence-dependent Kink-and-Slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove. J. Biomol. Struct. Dyn. 27, 843-59 (2010).

Pinto I.G., Guilbert C., Ulyanov N.B., Stearns J. & James T.L. Discovery of ligands for a novel target, the human telomerase RNA, based on flexible-target virtual screening and NMR. J. Med. Chem. 27, 7205-15 (2008).

Ulyanov N.B., Shefer K., James T.L. & Tzfati Y. Pseudoknot structures with conserved base triples in telomerase RNAs of ciliates. Nucl. Acids Res. 35, 6150-60 (2007).

Shefer K., Brown Y., Gorkovoy V., Nussbaum T., Ulyanov N.B. & Tzfati Y. A triple helix within a pseudoknot is a conserved and essential element of telomerase RNA. Mol. Cell. Biol. 27, 2130-43 (2007).

Mujeeb A., Ulyanov N.B., Georgantis S., Smirnov I., Chung J., Parslow T.G. & James T.L. Nucleocapsid protein-mediated maturation of dimer initiation complex of full-length SL1 stemloop of HIV-1: sequence effects and mechanism of RNA refolding. Nucl. Acids Res. 35, 2026-34 (2007).

Ulyanov N.B., Mujeeb A., Du Z., Tonelli M., Parslow T.G. & James T.L. NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site. J. Biol. Chem. 281, 16168-77 (2006).

Beniaminov A.D., Samokhin A.B., Ulyanov N.B. & Minyat E.E. Characteristics of two-step RNA dimerization in avian sarcoma and leukosis viruses. Molecular Biology 39, 130-136 (2005) (Engl. transl.)

Du Z., Yu J., Ulyanov N.B., Andino R. & James T.L. Solution structure of a consensus stem-loop D RNA domain that plays important roles in regulating translation and replication in enteroviruses and rhinoviruses. Biochemistry 43, 11959-72 (2004).

Du Z., Ulyanov N.B., Yu J., Andino R. & James T.L. NMR structures of loop B RNAs from the stem-Loop IV domain of the Enterovirus internal ribosome enrty site: A single C to U substitution drastically changes the shape and flexibility of RNA. Biochemistry 43, 5757-71 (2004).

Tonelli M., Ulyanov N.B., Billeci T.M., Karwowski B., Guga P., Stec W.J. & James T.L. Dynamic NMR structures of [Rp]- and [Sp]-phosphorothioated DNA-RNA hybrids: Is flexibility required for RNase H recognition? Biophys. J. 85, 2525-38 (2003).

Beniaminov A.D., Ulyanov N.B., Samokhin A.B., Ivanov V.I., Du Z. & Minyat E.E. The role of structural elements in dimerization of RNA fragments in avian retroviruses. Molecular Biology 37, 446-455 (2003) (Engl. transl.)

Comolli L.R., Ulyanov N.B., Soto A.M., Marky L.A., James T.L. & Gmeiner W.H. NMR structure of the 3' stem-loop from human U4 snRNA. Nucl. Acids Res. 30, 4371-79 (2002).

Ulyanov N.B., Bauer W.R. & James T.L. High-resolution NMR structure of an AT-rich DNA sequence. J. Biomolec. NMR 22, 265-80 (2002).

Kojima C., Ulyanov N.B., Kainoshi M. & James T.L. Slow motion in the CAA:TTG sequence of a DNA decamer duplex studied by NMR. Biochemistry 40, 7239-46 (2001).

Aramini J.M., Mujeeb A., Ulyanov N.B. & Germann M.W. Conformational dynamics in mixed alpha/beta-oligonucleotides containing polarity reversals: a molecular dynamics study using time-averaged restraints. J. Biomolec. NMR 18, 287-302 (2000).

Görler A., Ulyanov N.B. & James T.L. Determination of the populations and structures of multiple conformers in an ensemble from NMR data: multiple-copy refinement of nucleic acid structures using floating weights. J. Biomolec. NMR 16, 147-64 (2000).

Liu H., Farr-Jones S., Ulyanov N.B., Llinas M., Marqusee S., Groth D., Cohen F.E., Prusiner S.B. & James T.L. Solution structure of syrian hamster prion protein rPrP(90-231). Biochemistry 38, 5362-77 (1999).

Ivanov V.I., Bondarenko S.A., Zdobnov E.M., Beniaminov A.D., Minyat E.E. & Ulyanov N.B. A pseudoknot-compatible universal site is located in the large ribosomal RNA in the peptidyltransferase center. FEBS Lett. 446 60-64 (1999).

Schmitz U., Donati A., James T.L., Ulyanov N.B. & Yao L. Small structural ensembles for a 17-nucleotide mimic of the tRNA T-psi-C loop via fitting dipolar relaxation rates with the quadratic programming algorithm. Biopolymers 46 329-42 (1998).

Ulyanov N.B., Ivanov V.I., Minyat E.E., Khomyakova E.B., Petrova M.V., Lesiak K. & James T.L. A pseudosquare knot structure of DNA in solution. Biochemistry 37 12715-26 (1998).

Donati A., Rossi C., Martini S., Ulyanov N.B. & James T.L. NOE intensities from multiple conformations in solution analyzed by the complete relaxation matrix approach. Appl. Magn. Reson. 15, 401-406 (1998).

James T.L., Liu H., Ulyanov N.B., Farr-Jones S., Zhang H., Donne D.G., Kaneko K., Groth D., Mehlhorn I., Prusiner S.B. & Cohen F.E. Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform. Proc. Natl. Acad. Sci. U.S.A. 94 10086-91 (1997).

Ulyanov N.B. & James T.L. Statistical analysis of DNA duplex structural features. Methods Enzymol. 261 90-120 (1995).

Ulyanov N.B., Schmitz U., Kumar A. & James T.L. Probability assessment of conformational ensembles: Sugar repuckering in a DNA duplex in solution. Biophys. J. 68 13-24 (1995).

Liu H., Spielmann H.P., Ulyanov N.B., Wemmer, D.E. & James T.L. Interproton distance bounds from 2D NOE intensities: effect of experimental noise and peak integration errors. J. Biomolec. NMR 6, 390-402 (1995).

Ulyanov N.B., Bishop K.D., Ivanov V.I. & James T.L. Tertiary base pair interactions in slipped loop-DNA: an NMR and model building study. Nucl. Acids Res. 22, 4242-9 (1994).

Zhurkin V.B., Raghunathan G., Ulyanov N.B., Camerini-Otero R.D. & Jernigan R.L. A parallel DNA triplex as a model for the intermediate in homologous recombination. J. Mol. Biol. 239, 181-200 (1994).

Ulyanov N.B. & James T.L. Statistical analysis of DNA duplex structures in solution derived by high resolution NMR. Appl. Magn. Reson. 7, 21-42 (1994).

Ulyanov N.B., Schmitz U. & James T.L. Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure. J. Biomolec. NMR 3, 547-68 (1993).

Schmitz U., Ulyanov N.B., Kumar A. & James T.L. Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data. J. Mol. Biol. 234, 373-89 (1993).

Ulyanov N.B., Sarma M.H., Zhurkin V.B. & Sarma R.H. Decreased interstrand H2-H1' distance in the GC-rich part of the duplex d(CCTCAAACTCC):d(GGAGTTTGAGG) in solution at low temperature: proton nuclear magnetic resonance investigation. Biochemistry 32, 6875-83 (1993).

Ulyanov N.B., Gorin A.A., Zhurkin V.B., Chen B.-C., Sarma M.H. & Sarma R.H. Systematic study of Nuclear Overhauser Effects vis-a-vis local helical parameters, sugar puckers, and glycosidic torsions in B DNA: Insensitivity of NOE to local transitions in B DNA oligonucleotides due to internal structural compensations. Biochemistry 31 3918-30 (1992).

Zhurkin V.B., Ulyanov N.B., Gorin A.A. & Jernigan R.L. Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc. Natl. Acad. Sci. U.S.A. 88 7046-50 (1991).

Alexandrova N.M., Itkes A.V., Imamova L.R., Chernov B.K., Tulchinsky E.M., Ulyanov N.B. & Kisselev L.L. Human c-myc gene contains a regulatory site similar to consensus of interferon response sequence (IRS). FEBS Lett. 265 67-70 (1990).

Ulyanov N.B. & Zhurkin V.B. Sequence-dependent anisotropic flexibility of B-DNA. A conformational study. J. Biomolec. Struct. Dynam. 2 361-85 (1984).

Logofet D.O. & Ulianov N.B. Sign stability in model ecosystems - a complete class of sign-stable patterns. Ecol. Model. 16 173-89 (1982).