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RNA Structure and Folding

Protein-Nucleic Acid Interactions

Reviews and Methodology

  • Shcherbakova, I. Mitra, S., Beer, R. & Brenowitz, M. (2007) Following molecular transitions with single residue spatial and millisecond time resolution in Biophysical Tools for Biologists Volume 1, J.J. Correia and H.W. Detrich editors, Elsevier / Academic Press, in press.

  • Khrapunov, S., Brenowitz, M., Rice, P. & Catalano, C.E. (2006) Binding then bending: A mechanism for wrapping DNA [Invited commentary], Proc. Natl. Acad. Sci. 103(51), 19217 - 8. [Abstract] [Full Text]

  • Shcherbakova, I., Mitra, S., Beer, R. & Brenowitz M. (2006) Fast Fenton footprinting: A laboratory-based method for the time-resolved analysis of DNA, RNA and proteins, Nucleic Acids Research 34(6), e48. <a target="_blank" href="">[Abstract]</a> <a target="_blank" href="">[Full Text]</a>

  • Brenowitz, M., Erie, D.A. & Chance, M.R. (2005) Catching RNA polymerase in the act of binding: Intermediates in transcription illuminated by synchrotron footprinting [Invited commentary], Proc. Natl. Acad. Sci. 102, 4659 – 4660.<a target="_blank" href="">[Abstract]</a> <a target="_blank" href="/mbrenowitz/Papers/Brenowitz-Erie-Chance-PNAScommentary2005.pdf">[Full Text]</a>

  • Takamoto, K., Chance, M.R. & Brenowitz, M. (2004) Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions, Nucleic Acids Research (Methods), in press. <a target="_blank" href="">[Abstract]</a> <a target="_blank" href="/mbrenowitz/Papers/Takamoto-Chance-Brenowitz-NAR2004.pdf">[Full Text]</a>

  • Dhavan, G.M., Chance, M.R. & Brenowitz, M. (2003) Kinetics Analysis of DNA-Protein Interactions by Time Resolved Synchrotron X-ray Footprinting, in Kinetic Analysis of Macromolecules: A Practical Approach, K.A. Johnson ed., IRL Press at Oxford University Press, Oxford, pgs. 75 - 86.

  • Brenowitz, M., Chance, M.R., Dhavan, G.D. and Takamoto, K. (2002) Probing the structural dynamics of nucleic acid structure by quantitative time-resolved and equilibrium hydroxyl radical “footprinting”, Current Opinion in Structural Biology 12, 648 - 653. [Please email <a href=""></a> for a pdf]

  • Dhavan, G.M., Mollah, A.K.M.M. & Brenowitz, M. (2002) Equilibrium and Kinetic Quantitative DNase I Footprinting, Advances in DNA Sequence Specific Agents, Volume 4, 139 – 155, Elsevier Science (G.B. Jones, editor).

  • Woodson, S.A., Deras, M.L. & Brenowitz, M. (2001) Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays, Current Protocols in Nucleic Acid Chemistry, Unit 11.6, pgs 11.6.1 – 11.6.23.

  • Maleknia SD, Ralston CY, Brenowitz MD, Downard KM, Chance MR (2001) Determination of Macromolecular Folding and Structure by Synchrotron X-Ray Radiolysis Techniques, Analytical Biochem.istry 289, 103 – 115. <a href="">[Abstract]</a> <a href="/mbrenowitz/Papers/maleknia-ralston-brenowitz-downard-chance-2001.pdf">[Full Text]</a>

  • Mollah, A.K.M.M. & Brenowitz, M. (2000) Quantitative DNase I Kinetics Footprinting. Protein-DNA Interactions – a Practical Approach, A. Travers & M. Buckle eds., IRL Press at Oxford University Press, Oxford, 281 - 290.

  • Ralston, C.Y., Sclavi, B., Sullivan, M., Deras, M.L., Woodson, S.A., Chance, M.R., Brenowitz, M. (2000) Time-resolved synchrotron X-ray footprinting and its application to RNA folding, Meth. Enz. 317, 353 - 368. 

  • Maleknia, S.D., Brenowitz, M. & Chance, M.R. (1999) Millisecond Radiolytic Modification of Peptides by Synchrotron X-rays Identified by Mass Spectrometry, Analytical Chemistry 71, 3965 - 73. <a href="">[Abstract]</a> <a href="/mbrenowitz/Papers/maleknia-brenowitz-chance-1999.pdf">[Full Text]</a>

  • Sclavi, B., Sullivan, M., Woodson, S., Chance, M., & Brenowitz, M. (1998) Following the Folding of RNA with Time-resolved Synchrotron X-ray “Footprinting”. Meth. Enzymol. 295, 379 - 402.

  • Petri, V. & Brenowitz, M. (1997) Quantitative nucleic acids footprinting - thermodynamic and kinetic approaches. Current Opinion in Biotechnology 8(1), 36 - 44. <a href="">[Abstract]</a> <a href="/mbrenowitz/Papers/Petri&Brenowitz-CurrOpin1997.pdf">[Full Text]</a>

  • Hsieh, M. & Brenowitz, M. (1996) Quantitative Kinetics Footprinting of Protein-DNA Association Reactions. Meth. Enzymol. 274, 478 - 492.