John P. Marino
	Ph.D. Chemistry, Yale University, 1995 Adjunct Assistant Professor University of Maryland Biotechnology Institute Center for Advanced Research in Biotechnology 9600 Gudelsky Dr. Rockville, MD 20850 USA Phone: (301)-738-6160 FAX: (301)-738-6255 E-mail: marino@carb.nist.gov Research Interests:  Biomolecular NMR spectroscopy applied to understanding RNA-RNA and RNA-Protein Interactions.

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How ribonucleic acid (RNA) molecules fold into secondary and tertiary structures and how protein binding is involved in specific RNA functions are fundamental questions central to understanding many biochemical processes. The research in our laboratory focuses on using multi-dimensional heteronuclear NMR spectroscopy, together with other biophysical techniques, to study the structure and dynamics of RNA and RNA-protein complexes in solution. Using NMR derived structural/dynamical information, we hope to gain an insight into the underlying RNA/protein biochemistry that will guide further chemical analysis and aid in the "rational-based" design of therapeutics.

RNA Structure and RNA-Protein Interactions:

Some of the current projects in the lab focus on studying the structure of RNA loop-loop "kissing" interactions. Such interactions have been found to be critical in certain RNA folds and antisense-based RNA regulation systems. One "kissing" interaction we are studying is derived from the R1 plasmid RNA antisense translational control system. In the R1 system, the anti-sense RNA (Cop A) acts as the main copy number control element by specifically binding to its target, the leader region of the RepA mRNA (CopT), and inhibiting the synthesis of the initiator protein, RepA. A second system we are investigating is the dimerization initiation site (DIS) of the HIV-1 genome. The dimerization of the genomic RNA of human immunodeficiency type I (HIV-1) is an event that is thought to control crucial steps in HIV-1 replication. We are studying a homodimeric "kissing" interaction that is proposed to be initially formed by a hairpin found within the DIS region of the HIV genome.

In collaboration with the laboratories of Donald M. Crothers and Lynne Regan (Yale University) we are studying the complex formed between the ColE1 plasmid encoded protein ROM and a "kissing" complex formed between hairpins derived from the RNA I and RNA II transcripts of the ColE1 plasmid. In addition, we are studying complexes formed between the ROM protein and "kissing" complexes, with loops of varying size and sequence, to attempt to elucidate the molecular basis for recognition of RNA by ROM mutants with altered binding specificity.

Biomolecular NMR Spectroscopy:

Our lab is also interested in the development of new heteronuclear NMR methods for improving existing experiments and for acquiring new structural and dynamical information. Current projects are focused on heteronuclear NMR methods applied to nucleic acids and include efforts to develop methods for determining J-couplings, for using sensitivity enhanced MQ correlation and for measuring residual dipolar couplings.