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1.
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Shcherbakova I, Mitra S. Hydroxyl-radical footprinting to probe equilibrium changes in RNA tertiary structure. Methods Enzymol. 2009; 468:31-46.
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2.
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Simmons K, Martin JS, Shcherbakova I, Laederach A. Rapid quantification and analysis of kinetic •OH radical footprinting data using SAFA. Methods Enzymol. 2009; 468:47-66.
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3.
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Shcherbakova I, Mitra S, Laederach A, Brenowitz M. Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. Curr Opin Chem Biol. 2008 Dec; 12(6):655-66.
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4.
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Sprouse RO, Shcherbakova I, Cheng H, Jamison E, Brenowitz M, Auble DT. Function and structural organization of Mot1 bound to a natural target promoter. J Biol Chem. 2008 Sep 5; 283(36):24935-48.
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5.
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Mitra S, Shcherbakova IV, Altman RB, Brenowitz M, Laederach A. High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res. 2008 Jun; 36(11):e63.
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6.
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Shcherbakova I, Mitra S, Beer RH, Brenowitz M. Following molecular transitions with single residue spatial and millisecond time resolution. Methods Cell Biol. 2008; 84:589-615.
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7.
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Shcherbakova I, Brenowitz M. Monitoring structural changes in nucleic acids with single residue spatial and millisecond time resolution by quantitative hydroxyl radical footprinting. Nat Protoc. 2008; 3(2):288-302.
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8.
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Laederach A, Shcherbakova I, Jonikas MA, Altman RB, Brenowitz M. Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding. Proc Natl Acad Sci U S A. 2007 Apr 24; 104(17):7045-50.
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9.
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Shcherbakova I, Mitra S, Beer RH, Brenowitz M. Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res. 2006; 34(6):e48.
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10.
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Laederach A, Shcherbakova I, Liang MP, Brenowitz M, Altman RB. Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J Mol Biol. 2006 May 12; 358(4):1179-90.
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11.
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Kwok LW, Shcherbakova I, Lamb JS, Park HY, Andresen K, Smith H, Brenowitz M, Pollack L. Concordant exploration of the kinetics of RNA folding from global and local perspectives. J Mol Biol. 2006 Jan 13; 355(2):282-93.
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12.
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Shcherbakova I, Brenowitz M. Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure. J Mol Biol. 2005 Nov 25; 354(2):483-96.
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13.
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Shcherbakova I, Gupta S, Chance MR, Brenowitz M. Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme. J Mol Biol. 2004 Oct 1; 342(5):1431-42.
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