Publications

Displaying 51 - 75 of 79

Probing Anomalous Structural Features in Polypurine Tract-Containing RNA-DNA Hybrids with Neomycin B

July 28, 2009

Author(s)

Robert G. Brinson, Kevin Turner, Hye Y. Yi-Brunozzi, Stuart F. Le Grice, Daniele Fabris, John P. Marino

During (-)-strand DNA synthesis in retroviruses and Saccharomyces cerevisiae LTR-retrotransposons, a purine rich region of the RNA template, known as the polypurine tract (PPT) is resistant to RNase H-mediated hydrolysis and subsequently serves as a primer

NMR Analysis of Rhodopsin-Transducin Interactions

December 1, 2006

Author(s)

Kevin Ridge, John Marino, T Ngo, Eva Ramon, D M. Brabazon, N G. Abdulaev

Heterotrimeric G-protein activation by an agonist-stimulated G-protein coupled receptor (R*) requires the propagation of structural signals from the receptor interacting surfaces to the guanine nucleotide-binding pocket. Employing high-resolution NMR

Conformational Changes Associated With Receptor-Stimulated Guanine Nucleotide Exchange in a Heterotrimeric G-Protein a-Subunit: NMR Analysis of the GTPgS-Bound States

March 17, 2006

Author(s)

K D. Ridge, N G. Abdulaev, Xi-Cheng Zhang, T Ngo, D M. Brabazon, John P. Marino

Solution NMR studies of a 15N-labeled G-protein ?-subunit (G?) chimera (15N-ChiT) reconstituted heterotrimer have previously shown that binding of ??-subunits induces a pre-activated conformation in G? that may facilitate interaction with R* and guanine

Examining Ty3 Polypurine Tract Structure and Function by Nucleoside Analog Interference

February 1, 2006

Author(s)

Chandravanu Dash, John Marino, Stuart F. Le Grice

Although retroviral and LTR-retrotransposon PPTs differ significantly in both their length and sequence, they are accurately removed from (+) RNA and (+) DNA by their cognate RTs, suggesting common structural features of these RNA/DNA hybrids contribute to

A Ribose Sugar Conformational Switch in the LTR-Retrotransposon Ty3 Polypurine Tract-Containing RNA/DNA Hybrid

November 30, 2005

Author(s)

Hye Y. Yi-Brunozzi, D M. Brabazon, Daniela Lener, Stuart F. LeGrice, John Marino

To probe structural features of a polypurine-tract (PPT) that mediate its specific recognition and processing, a model 20bp RNA/DNA duplex, which includes the full PPT sequence of the saccharomyces cerevisiae LTR-retrotransposon Ty3, has been investigated

Heterotrimeric G-protein alpha-Subunit Adopts a "Preactivated" Conformation When Associated with beta-Subunits

August 29, 2005

Author(s)

N G. Abdulaev, T Ngo, C Zhang, A Dinh, D M. Brabazon, K D. Ridge, John P. Marino

Bacterial Expression and One-Step purification of an isotope-labeled heterotremic G-protein a-subunit

May 1, 2005

Author(s)

John P. Marino, N G. Abdulaev, C Zhang, A Dinh, T Ngo, P N. Bryan, D M. Brabazon, K D. Ridge

Bacterial Expression and One-Step Purification of an Isotope-Labeled Heterotrimeric G-Protein alpha-Subunit

May 1, 2005

Author(s)

N G. Abdulaev, Xi-Cheng Zhang, Andy Dinh, T Ngo, Phillip Bryan, D M. Brabazon, John Marino, Kevin Ridge

Heterologous expression systems are often employed to generate sufficient quantities of isotope-labeled proteins for high-resolution NMR studies. Recently, the interaction between the prodomain region of subtilisin and an active, mutant form of the mature

Single Molecule Fluorescence Resonance Energy Transfer of a RNA Kissing Complex

January 27, 2005

Author(s)

Peter Yim, Xiaoyi Y. Zhang, E S. DeJong, J M. Carroll, John P. Marino, Lori S. Goldner

We used single molecular fluorescence resonance energy transfer (FRET) to understand the conformation of a RNA loop to loop complex, termed a kissing complex. The kissing complex formed by two Escherichia Coli (ColE1) plasmid-encoded transcripts, RNA I and

A Proton-Coupled Dynamic Switch in the HIV-1 Dimerization Initiation Site Kissing Complex

February 1, 2004

Author(s)

M Mihailescu, John Marino

In human immunodeficiency virus type 1 (HIV-1), the dimerization initiation site (DIS) is the sequence primarily responsible for initiating the non-covalent linkage of two homologous strands of genomic RNA during viral assembly. The DIS loop contains an

Homonuclear Hartmann-Hahn Transfer With Reduced Relaxation Losses by Use of the MOCCA-XY16 Multiple Pulse Sequence

January 1, 2004

Author(s)

J Furrer, F Kramer, John Marino, S J. Glaser, B. Luy

Proflavine Acts as a Rev Inhibitor by Targeting the High-Affinity Rev Binding Site of the Rev-Responsive Element of HIV-1

July 8, 2003

Author(s)

E S. DeJong, C Chang, M K. Gilson, John Marino

Rev is an essential regulatory HIV-1 protein that binds the Rev Responsive Element (RRE) within the env gene of the HIV-1 RNA genome, activating the switch between viral latency and active viral replication. Previously, we have shown that selective

Evidence for Structural Changes in Carboxyl-Terminal Peptides of Transducin Alpha-Subunit Upon Binding a Soluble Mimic of Light-Activated Rhodopsin

January 21, 2003

Author(s)

D M. Brabazon, N G. Abdulaev, John Marino, K D. Ridge

Although a high-resolution crystal structure for the ground state of rhodopsin is now available, portions of the cytoplasmic surface are not well resolved and the structural basis for the interaction of the cytoplasmic loops with the retinal G-protein

JE-TROSY: combined J- and TROSY-spectroscopy for the measurement of one-bond couplings in macromolecules

January 1, 2003

Author(s)

B. Luy, John Marino

Since the recent introduction of the use of residual dipolar couplings in high-resolution NMR studies of macromolecules, there has been a renewed interest in rapid, sensitive methods for the measurement of 15N- 1H} and 13C- 1H} one-bond couplings. For

Mechanism of Nucleocapsid Protein Catalyzed Structural Isomerization of the Dimerization Initiation Site of HIV-1

December 17, 2002

Author(s)

M J. Rist, John Marino

Dimerization of two homologous strands of genomic RNA is an essential feature of retroviral replication. In the human immunodeficiency virus type I (HIV-1), a conserved stem-loop sequence, the dimerization initiation site (DIS), has been identified as the

Observation of H-Bond Mediated 3h J H2H3 Coupling Constants Across Watson-Crick AU Base Pairs in RNA

October 1, 2002

Author(s)

B. Luy, U Richter, E S. DeJong, O W. Sorensen, John Marino

3hJ H2H3 trans-hydrogen bond scalar couplings have been observed for the first time in Watson-Crick AU base pairs in uniformly 15N-labeled RNA oligonucleotides using a new 2hJ NN-HNN-E.COSY experiment. The experiment, utilizes adenosine H2 (AH2) for

Fluorescent Nucleotide Base Analogs as Probes of Nucleic Acid Structure, Dynamics and Interactions

August 1, 2002

Author(s)

M J. Rist, John Marino

Highly fluorescent nucleotide base analogs provide sensitive probes for studying the structure, dynamics and interactions of nucleic acids. These analogs can be incorporated site-specifically into oligonucleotides through standard automated synthetic

RNA and RNA-Protein Complexes as Targets for Therapeutic Intervention

May 1, 2002

Author(s)

E S. DeJong, B. Luy, John Marino

Today, the majority of pharmaceuticals developed to treat cancers and viral/bacterial infections target cellular, bacterial or viral proteins known to be associated with a given pathology. Although proteins are the focus of most current drug discovery

1 H- 31 P CPMG-Correlated Experiments for the Assignment of Nucleic Acids

November 14, 2001

Author(s)

B. Luy, John Marino

Phosphorus (31P) nuclear magnetic resonance (NMR) spectroscopy can provide important information about the structure and dynamics of nucleic acids in solution. The application of 31P NMR, however, often requires the difficult task of resolving and

S 3 E-E.COSY Methods for the Measurement of 19 F Associated Scalar and Dipolar Coupling Constants

September 1, 2001

Author(s)

B. Luy, J J. Barchi, John Marino

A 1H-19F spin state selective excitation (S3E) pulse sequence element has been applied in combination with 1H homonuclear mixing to create E.COSY-type experiments designed to measure scalar JHF2' and JHH2' and residual dipolar DHF2' and DHH2' couplings in

Single Molecule Probes

August 1, 2001

Author(s)

Lori S. Goldner, K D. Weston, W F. Heinz, Jeeseong Hwang, E S. DeJong, John P. Marino

The technology to rapidly manipulate and screen individual molecules lies at the frontier of measurement science and impacts emerging bio- and nano-technologies. Fundamental biological and chemical processes can now be probed with unprecedented detail, one

Association of an RNA Kissing Complex Analyzed Using 2-Aminopurine Fluorescence

June 1, 2001

Author(s)

M J. Rist, John Marino

The fluorescent probe, 2-aminopurine-2'-O-methyl riboside (2-AP) has been selectively incorporated at adenosine positions in stem-loops (so called R1inv and R2inv), derived from the ColE1 plasmid encoded RNA I and RNA II transcripts, that interact to form

Measurement and Application of 1 H- 19 F Dipolar Couplings in the Structure Determination of 2'-Fluorolabeled RNA

May 1, 2001

Author(s)

B. Luy, John Marino

Residual dipolar couplings can provide powerful restraints for determination and refinement of the solution structure of macromolecules. The application of these couplings in nucleic acid structure elucidation can have an especially dramatic impact since

Direct Evidence for Watson-Crick Base Pairs in a Dynamic Region of RNA Structure

August 23, 2000

Author(s)

B. Luy, John Marino

Trans-H-bond 2hJ N1N3 scalar couplings were measured for the RNA hairpin, CopA29, which is derived from the R1 plasmid encoded RNA transcript, CopA, 21 using a dual-detected uracil H3/adenine-H2 (UH3/AH2) J nn HNN-COSY (see supporting Information for

Mechanism of Neomycin and Rev Peptide Binding to the Rev Responsive Element of HIV-1 as Determined by Fluorescence and NMR Spectroscopy

May 16, 2000

Author(s)

K Lacourciere, J T. Stivers, John Marino

Rev is an essential HIV-1 regulatory protein that binds the Rev Responsive Element (RRE) within the env gene of the HIV-1 RNA genome and is involved in transport of unspliced or partially spliced viral mRNA from the cell nucleus to the cytoplasm. Previous

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