In previous work the rate of isotopic hydrogen exchange of the purine ring was determined for a collection of mono-, oligo-, and polynucleotide structures using techniques of laser Raman spectroscopy. The exchange kinetics were correlated with the type of nucleotide, the molecular conformation, and the hydrogen bonding interactions of the purine ring. It was determined that the exchange rate can be employed to monitor the kind and amount of DNA or RNA secondary structure, including the number of strands in multi-stranded helices and the presence of Hoogsteen-type interactions. The solvent accessibility of the 7N ring site has emerged as a particularly influential factor in determining the kinetics of 8C-H exchange. In the proposed work the Raman dynamic probe will be exploited to determine the molecular environment of A and G residues of viral RNA and DNA in native plant and bacterial viruses, and in partially assembled and mutant virions. We shall also investigate several well characterized nucleoprotein complexes, such as the fd virus gene 5 protein-DNA complex, the phage lambda (cI and Cro) repressor-operator and E. coli lac repressor-operator systems. The kinetic studies will be augmented with equilibrium Raman studies to determine changes in DNA and RNA structure which may accompany protein binding. These investigations will provide new information on the nature of protein-nucleic acid interactions which are important for virus assembly and stability, and for gene regulation. The project will improve our understanding of the nature of protein/nucleic acid recognition. We shall employ the powerful techniques of optical multichannel analysis and Fourier deconvolution for rapid and accurate data acquisition and analysis. The proposed applications will advance the use of laser Raman spectroscopy both as a complement to other structure-determining methods and as a quantitative probe of nucleic acid structures and dynamics.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI018758-08
Application #
3128166
Study Section
Biophysics and Biophysical Chemistry B Study Section (BBCB)
Project Start
1987-09-01
Project End
1990-08-31
Budget Start
1988-09-01
Budget End
1989-08-31
Support Year
8
Fiscal Year
1988
Total Cost
Indirect Cost
Name
University of Missouri Kansas City
Department
Type
Overall Medical
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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