The broad, long term objective of the project is to deepen understanding of how the electrically charged phosphate groups of the DNA molecule influence the structure of DNA, the interactions of DNA molecules among themselves and with small ions and drugs, and the interactions of DNA with proteins, especially the DNA-protein complexes involved in the genetic apparatus.
The specific aims are to find an electrostatic potential of a polyion, for example, DNA, that accurately describes long-range ionic interaction; to extend this potential to handle interactions among two or more parallel rodlike polyionic segments, with the aims of understanding experimentally observed formation of clusters of identically changed polyions, such as polylysine, DNA and synthetic charged polymers; and to apply the potential in the description of the elasticity driven transitions of the nucleosome (the structural unit of the chromosomes). The methods used are the theoretical tools of statistical mechanics, in particular the methods of counterion condensation theory, which has been developed primarily by the group and has been an important influence on how ionic interactions are presently understood.
|Kosikov, Konstantin M; Gorin, Andrey A; Lu, Xiang-Jun et al. (2002) Bending of DNA by asymmetric charge neutralization: all-atom energy simulations. J Am Chem Soc 124:4838-47|
|Manning, Gerald S (2002) Electrostatic free energy of the DNA double helix in counterion condensation theory. Biophys Chem 101-102:461-73|
|Volker, J; Klump, H H; Manning, G S et al. (2001) Counterion association with native and denatured nucleic acids: an experimental approach. J Mol Biol 310:1011-25|
|Manning, G S; Ray, J (1998) Counterion condensation revisited. J Biomol Struct Dyn 16:461-76|
|Fenley, M O; Manning, G S; Marky, N L et al. (1998) Excess counterion binding and ionic stability of kinked and branched DNA. Biophys Chem 74:135-52|
|Manning, G S (1995) An elastic model for conformational transitions of spacer DNA in chromatin;first results. J Biomol Struct Dyn 12:1083-101|
|Fenley, M O; Olson, W K; Tobias, I et al. (1994) Electrostatic effects in short superhelical DNA. Biophys Chem 50:255-71|
|Manning, G S (1993) An elastic model for in-plane deformations of small DNA rings. J Biomol Struct Dyn 10:657-73|
|Ray, J; Manning, G S (1992) Theory of delocalized ionic binding to polynucleotides: structural and excluded-volume effects. Biopolymers 32:541-9|
|Marky, N L; Manning, G S (1991) The elastic resilience of DNA can induce all-or-none structural transitions in the nucleosome core particle. Biopolymers 31:1543-57|
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