Fall 2005
Seminar Class in Molecular Biophysics
Theme: "Electrostatic Effects
in
Biomolecular Structures"
Course Coordinator:
Wilma K. Olson - (732) 445-3993
olson@rutchem.rutgers.edu
Syllabus
List of Student Presentations
Reading Assignments:
Information will be posted as it becomes available.
Primary readings are
highlighted
with larger print
Tigran V. Chalikian
Tigran V. Chalikian and Kenneth J. Breslauer, (1998) "Volumetric properties of nucleic acids", Biopolymers (Nucleic Acid Sciences), Vol. 48, 264-280
Tigran V. Chalikian, Jens Völker, A. R. Srinivasan, Wilma K. Olson and Kenneth J. Breslauer, (1999) "The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques", Biopolymers, Vol. 50, 459-471
Adrian Lee and Tigran V. Chalikian, (2001) "Volumetric characterization of the hydration properties of heterocyclic bases and nucleosides", Biophysical Chemistry 92 209 227
Anna Tikhomirova and Tigran V. Chalikian, (2004) "Probing hydration of monovalent cations condensed around polymeric nucleic acids", J. Mol. Biol. 341, 551-563
David D. Dunlap
Claudio Rivetti, Martin Guthold and Carlos Bustamante, (1996), "Scanning Force Microscopy of DNA Deposited onto Mica: Equilibration versus Kinetic Trapping Studied by Statistical Polymer Chain Analysis", J. Mol. Biol. 264, 919-932
Gerald S. Manning, (2003) "Comments on Selected Aspects of Nucleic Acid Electrostatics", Biopolymers , Vol. 69, 137-143
Marcia O. Fenley
Record, MT, Lohman, T. M. and deHaseth, P., (1976) "Ion effects on ligand-nucleic acid interactions", J. Mol. Biol. 107:145-158
Nancy L. Marky and Gerald S. Manning, (2000) "An interpretation of small-ion effects on the electrostatics of the ì repressor DNA complex", J. Am. Chem. Soc. , 122, 6057-6066
Cuauhtémoc García-García and David E. Draper, (2003) "Electrostatic interactions in a peptide-RNA complex", J. Mol. Biol. 331, 75-88
Rajat Banerjee, Amit Kumar Mandal, Rajesh Saha, Soumi Guha, Soma Samaddar, Anusree Bhattacharyya and Siddhartha Roy, (2003) "Solvation change and ion release during aminoacylation by aminoacyl-tRNA synthetases", Nucleic Acids Research , Vol. 31, No. 20 6035±6042
Alexander H. Boschitsch, Marcia O. Fenley, (2004) "Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation", J Comput Chem 25: 935-955
Anand Jagota
Constantine Khripin, A. Jagota, C-Y.hung-Yuen Hui,(2005) "Electric fields in an electrolyte solution potential", to appear in the Journal of Chemical Physics
Steven Raymond Lustig, Anand Jagota, Constantine Khripin, and Ming Zheng, (2005) "Theory of structure-based carbon nanotube separations by ion-exchange chromatography of DNA/CNT hybrids", J. Phys. Chem. B, 109, 2559-2566
Ming Zheng, Anand Jagota, Michael S. Strano, Adelina P. Santos, Paul Barone,. Grace Chou, Bruce A. Diner, Mildred S. Dresselhaus, Robert S. Mclean, G. Bibiana Onoa, Georgii G. Samsonidze, Ellen D. Semke, Monica Usrey, Dennis J. Walls , (2003) "Structure-based carbon nanotube sorting by sequence-dependent DNA assembly", Science 302, 28 November
Gerald B. Koudelka
Steven A. Mauro, David Pawlowski, and Gerald B. Koudelka, (2003) "The Role of the Minor Groove Substituents in Indirect Readout of DNA Sequence by 434 Repressor", J. Biol. Chem. Vol. 278, No. 15, Issue of April 11, 12955-12960
Steven A. Mauro and Gerald B. Koudelka, (2004) "Monovalent Cations Regulate DNA Sequence Recognition by 434 Repressor", J. Mol. Biol . 340, 445-457
Sanford H. Leuba
Tomschik, M., Zheng, H., van Holde, K., Zlatanova, J. and Leuba, S. H., (2005) "Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by spFRET". Proc. Natl. Acad. Sci. USA 102, 3278-3283
Bennink, M. L., Leuba, S. H., Leno, G. H., Zlatanova, J., de Grooth, B. G. and Greve, J,, (2001) "Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers", Nature Struct. Biol. 8, 606-610
Leuba, S. H., Karymov, M. A., Tomschik, M., Ramjit, R., Smith, P., and Zlatanova, J., (2003) "Assembly of single chromatin fibers depends on the tension in the DNA molecule: magnetic tweezers study", Proc. Natl. Acad. Sci. USA 100, 495-500
James Maher
Becker et al., (2005) "Bacterial repression loops require enhanced DNA flexibility", Mol. Biol. 349:716-730
Ross et al., (2001) "HMG proteins and DNA flexibility in transcription activation", Mol. Cell. Biol. 21:6598-6605
Williams and Maher, (2000) "Electrostatic mechanisms of DNA", Annu. Rev. Biophys. Biomol. Struct. 29:497-521
Gerald S. Manning
Manning, (2003), "Comments on Selected Aspects of Nucleic Acid Electrostatics", Biopolymers, Vol. 69, 137-143
Manning, (1988) "Three Persistence Lengths for a Stiff Polymer with an Application to DNA B-Z Junctions", Biopolymers, Vol. 27, 1529-1542 [In this paper, the sections of interest are"Review of Persistence Length for Bending," "The Persistence Length for Twist," and "Persistence Length for Contraction/Extension." ]
Camille Ripoll
Marie-Claire Verdus, Michel Thellier and Camille Ripol, (1997) "Storage of environmental signals in flax. Their morphogenetic effect as enabled by a transient depletion of calcium", The Plant Journal 12(6), 1399-1410
Marc Tafforeau, Marie-Claire Verdus, Vic Norris, Glenn J.White, Mike Cole, Maurice Demarty, Michel Thellier, and Camille Ripoll, (2004) "Plant sensitivity to low intensity 105 Ghz electromagnetic radiation", Bioelectromagnetics 25:403-407
Camille Ripoll, Vic Norris, and Michel Thellier, (2004) "Ion condensation and signal transduction", BioEssays 26:549-557
Nancy C. Stellwagen
Stellwagen, N. C., Gelfi, C., Righetti, P. G., (1997) "The free solution mobility of DNA", Biopolymers 42, 687-703
Stellwagen, N. C., Magnusdottir, S., Gelfi, C., Righetti, P. G., (2001) "Preferential counterion binding to A-tract DNA oligomers", J. Mol.Biol 305, 1025-1033
Stellwagen, E., Stellwagen, N. C., (2002) "The free solution mobility of DNA in Tris-acetate-EDTA buffers of different concentrations, with and without added NaCl", Electrophoresis 23, 1935-1941
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