The objective of this project is to understand the physical mechanism of DNA condensation by multivalent cations, so as to understand better the factors controlling condensation in viruses and cells and in applications to nucleic acid preparation and genetic engineering. This requires elucidation of the mechanism and rate constants for the elementary steps in the condensation process, the intermolecular forces stabilizing the condensed state, the role of co-solvents, and the specific behavior, added to general principles, that modulates the action of particular condensing ligands and DNA sequences. It also raises questions about the conditions under which other polyelectrolytes, perhaps less highly charged and stiff than DNA, can also be induced to undergo condensation into discrete particles that may have health-related applications as well as fundamental interest.
Specific aims : Perform numerical modeling and interpretation of the kinetics of elementary processes in DNA condensation-initial nucleation and monomolecular collapse, intermediate time growth of toroidal particles, and longer-term secondary aggregation, to get an integrated mechanistic picture. Continue development of a theory of attractive forces between DNAs based on fluctuations of the counterion atmosphere, taking into account ligand spatial extent and the curvature of the DNA surface. Dr. Bloomfield will use this theory to understand the effects of excess condensing agent on energetics, and the transition between two-body and many-body forces in dense DNA arrays. Continue DNA condensation measurements in aqueous solutions of osmolytes, and combine them with statistical thermodynamic treatment of mixed solvent systems, to gain insight into the role of preferential solvation and dielectric effects in DNA condensation. Investigate DNA condensation by a broad range of cationic ligands, to gain insight into the effects of higher charge, charge distribution, and ligand mobility and steric character on the energetics and structure of tightly-packed DNA bundles. Investigate the effects on DNA condensation of biologically interesting repetitive sequences such as A-ttracts and triplet repeats associated with genetic diseases. Investigate co-condensation of large and small DNA molecules, and condensation of other biopolymers, such as RNA and polypeptides.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular and Cellular Biophysics Study Section (BBCA)
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University of Minnesota Twin Cities
Schools of Arts and Sciences
United States
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Kankia, Besik I (2004) Inner-sphere complexes of divalent cations with single-stranded poly(rA) and poly(rU). Biopolymers 74:232-9
Kankia, Besik I (2004) Optical absorption assay for strand-exchange reactions in unlabeled nucleic acids. Nucleic Acids Res 32:e154
Kankia, Besik I (2003) Binding of Mg2+ to single-stranded polynucleotides: hydration and optical studies. Biophys Chem 104:643-54
Kankia, Besik I (2003) Mg2+-induced triplex formation of an equimolar mixture of poly(rA) and poly(rU). Nucleic Acids Res 31:5101-7
Matulis, Daumantas; Rouzina, Ioulia; Bloomfield, Victor A (2002) Thermodynamics of cationic lipid binding to DNA and DNA condensation: roles of electrostatics and hydrophobicity. J Am Chem Soc 124:7331-42
Tang, Karen E S; Bloomfield, Victor A (2002) Assessing accumulated solvent near a macromolecular solute by preferential interaction coefficients. Biophys J 82:2876-91
Wenner, Jay R; Williams, Mark C; Rouzina, Ioulia et al. (2002) Salt dependence of the elasticity and overstretching transition of single DNA molecules. Biophys J 82:3160-9
Williams, Mark C; Rouzina, Ioulia; Bloomfield, Victor A (2002) Thermodynamics of DNA interactions from single molecule stretching experiments. Acc Chem Res 35:159-66
Williams, M C; Rouzina, I; Wenner, J R et al. (2001) Mechanism for nucleic acid chaperone activity of HIV-1 nucleocapsid protein revealed by single molecule stretching. Proc Natl Acad Sci U S A 98:6121-6
Matulis, D; Bloomfield, V A (2001) Thermodynamics of the hydrophobic effect. I. Coupling of aggregation and pK(a) shifts in solutions of aliphatic amines. Biophys Chem 93:37-51

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