The central objectives of this research is to elucidate the conformations, configurations and interactions of nuclei acids and nucleotide analogs in biological macromolecular assemblies. The methodology focuses on the application of Raman equilibrium and dynamic probes of nucleic acid structure and hydrogen isotope exchange kinetics.
The specific aims of the proposed research are: (1) To establish new Raman spectra/structure correlations which facilitate DNA and RNA structure determinations in biological assemblies. (2) To further develop the Raman dynamic probe for discrimination and resolution of structure sensitive exchange processes in nucleic acids and their complexes. (3) To apply the Raman methodologies to biological assemblies which cannot readily be investigated by other structural techniques. Realization of these aims will significantly advance our understanding of DNA (and RNA) packaging, conformation and interactions in viruses and cell nuclei. Information will also be obtained to advance our understanding of DNA molecular sites and secondary structure which may be involved in transcriptional regulation and gene expression. In the proposed equilibrium studies, we shall investigate model nucleic acids of known three dimensional structure (oligomeric DNA crystals solved by x-ray methods) for the purpose of expanding our library of spectra/structure correlations to include conformation-sensitive cytosine, adenine and phosphodiester vibrational modes. These empirical studies will be augmented with normal mode analyses. In the proposed dynamics studies, we shall investigate purine 8CH exchanges, at the level of individual nucleotides in DNA of defined sequence, in order to characterize the effects of base sequence on helix groove dimensions as manifested by solvent accessibility. The Raman dynamic probe will be further developed to distinguish the more rapid imino exchanges of base- paired structures. We shall continue our development of Raman single channel and multi-channel instrumentation for more rapid and accurate data acquisition from nucleic acids and their complexes. Fourier deconvolution, curve fitting and related data reduction protocols will be employed to optimize data analysis, refinement and interpretation.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI018758-14
Application #
2060766
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Project Start
1987-09-01
Project End
1995-07-31
Budget Start
1994-08-01
Budget End
1995-07-31
Support Year
14
Fiscal Year
1994
Total Cost
Indirect Cost
Name
University of Missouri Kansas City
Department
Biochemistry
Type
Schools of Medicine
DUNS #
800772162
City
Kansas City
State
MO
Country
United States
Zip Code
64110
Munks, Michael W; McKee, Amy S; Macleod, Megan K et al. (2010) Aluminum adjuvants elicit fibrin-dependent extracellular traps in vivo. Blood 116:5191-9
Russell, M P; Vohnik, S; Thomas Jr, G J (1995) Design and performance of an ultraviolet resonance Raman spectrometer for proteins and nucleic acids. Biophys J 68:1607-12
Duguid, J G; Bloomfield, V A; Benevides, J M et al. (1995) Raman spectroscopy of DNA-metal complexes. II. The thermal denaturation of DNA in the presence of Sr2+, Ba2+, Mg2+, Ca2+, Mn2+, Co2+, Ni2+, and Cd2+. Biophys J 69:2623-41
Miura, T; Benevides, J M; Thomas Jr, G J (1995) A phase diagram for sodium and potassium ion control of polymorphism in telomeric DNA. J Mol Biol 248:233-8
Thomas Jr, G J; Benevides, J M; Overman, S A et al. (1995) Polarized Raman spectra of oriented fibers of A DNA and B DNA: anisotropic and isotropic local Raman tensors of base and backbone vibrations. Biophys J 68:1073-88
Miura, T; Thomas Jr, G J (1995) Structure and dynamics of interstrand guanine association in quadruplex telomeric DNA. Biochemistry 34:9645-54
Miura, T; Thomas Jr, G J (1995) Raman spectroscopy of proteins and their assemblies. Subcell Biochem 24:55-99
Benevides, J M; Kukolj, G; Autexier, C et al. (1994) Secondary structure and interaction of phage D108 Ner repressor with a 61-base-pair operator: evidence for altered protein and DNA structures in the complex. Biochemistry 33:10701-10
Benevides, J M; Weiss, M A; Thomas Jr, G J (1994) An altered specificity mutation in the lambda repressor induces global reorganization of the protein-DNA interface. J Biol Chem 269:10869-78
Reilly, K E; Thomas Jr, G J (1994) Hydrogen exchange dynamics of the P22 virion determined by time-resolved Raman spectroscopy. Effects of chromosome packaging on the kinetics of nucleotide exchanges. J Mol Biol 241:68-82

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