Published in Nucleic Acids Res on March 05, 2004
Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev (2010) 2.16
Selective inhibition of HIV-1 reverse transcriptase-associated ribonuclease H activity by hydroxylated tropolones. Nucleic Acids Res (2005) 1.75
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HIV-1 reverse transcription. Cold Spring Harb Perspect Med (2012) 1.29
Fluorescent pyrimidine ribonucleotide: synthesis, enzymatic incorporation, and utilization. J Am Chem Soc (2007) 1.23
Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation. RNA (2006) 1.17
Effects of mutations in the G tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage. J Virol (2004) 1.06
Mutations in the U5 sequences adjacent to the primer binding site do not affect tRNA cleavage by rous sarcoma virus RNase H but do cause aberrant integrations in vivo. J Virol (2006) 1.05
Investigating local conformations of double-stranded DNA by low-energy circular dichroism of pyrrolo-cytosine. Proc Natl Acad Sci U S A (2005) 1.04
The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine. Nucleic Acids Res (2012) 1.03
An emissive C analog distinguishes between G, 8-oxoG, and T. Org Lett (2009) 0.97
High-resolution NMR analysis of the conformations of native and base analog substituted retroviral and LTR-retrotransposon PPT primers. Chem Biol (2008) 0.96
Reverse transcriptase in motion: conformational dynamics of enzyme-substrate interactions. Biochim Biophys Acta (2009) 0.95
Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands. Nucleic Acids Res (2008) 0.94
Purine analog substitution of the HIV-1 polypurine tract primer defines regions controlling initiation of plus-strand DNA synthesis. Nucleic Acids Res (2006) 0.89
Alternate polypurine tracts affect rous sarcoma virus integration in vivo. J Virol (2006) 0.89
DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies. Biophys J (2009) 0.86
Characterization of the C-Terminal Nuclease Domain of Herpes Simplex Virus pUL15 as a Target of Nucleotidyltransferase Inhibitors. Biochemistry (2016) 0.86
Examining the ribonuclease H primer grip of HIV-1 reverse transcriptase by charge neutralization of RNA/DNA hybrids. Nucleic Acids Res (2008) 0.85
Synthesis of nucleoside 5'-O-alpha,beta-methylene-beta-triphosphates and evaluation of their potency towards inhibition of HIV-1 reverse transcriptase. Org Biomol Chem (2010) 0.84
Enzymatic incorporation of emissive pyrimidine ribonucleotides. Chem Asian J (2009) 0.84
Probing Retroviral and Retrotransposon Genome Structures: The "SHAPE" of Things to Come. Mol Biol Int (2012) 0.80
A single-label phenylpyrrolocytidine provides a molecular beacon-like response reporting HIV-1 RT RNase H activity. Nucleic Acids Res (2009) 0.80
Functionalized tricyclic cytosine analogues provide nucleoside fluorophores with improved photophysical properties and a range of solvent sensitivities. Chemistry (2013) 0.80
Solid-Phase Synthesis of 5'-O-β,γ-Methylenetriphosphate Derivatives of Nucleosides and Evaluation of Their Inhibitory Activity Against HIV-1 Reverse Transcriptase. Tetrahedron Lett (2010) 0.79
Integration of rous sarcoma virus DNA: a CA dinucleotide is not required for integration of the U3 end of viral DNA. J Virol (2008) 0.78
Structural studies of RNA/DNA polypurine tracts. Chem Biol (2008) 0.76
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The use of diaminopurine to investigate structural properties of nucleic acids and molecular recognition between ligands and DNA. Nucleic Acids Res (1998) 1.20
Residues in the alphaH and alphaI helices of the HIV-1 reverse transcriptase thumb subdomain required for the specificity of RNase H-catalyzed removal of the polypurine tract primer. J Biol Chem (1999) 1.12
Mutational analysis of Tyr-501 of HIV-1 reverse transcriptase. Effects on ribonuclease H activity and inhibition of this activity by N-acylhydrazones. J Biol Chem (2001) 1.11
Role of the "helix clamp" in HIV-1 reverse transcriptase catalytic cycling as revealed by alanine-scanning mutagenesis. J Biol Chem (1996) 0.99
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Interaction of p55 reverse transcriptase from the Saccharomyces cerevisiae retrotransposon Ty3 with conformationally distinct nucleic acid duplexes. J Biol Chem (2000) 0.95
The 'helix clamp' in HIV-1 reverse transcriptase: a new nucleic acid binding motif common in nucleic acid polymerases. Nucleic Acids Res (1994) 0.94
Nonpolar thymine isosteres in the Ty3 polypurine tract DNA template modulate processing and provide a model for its recognition by Ty3 reverse transcriptase. J Biol Chem (2003) 0.94
Hydrolysis of RNA/DNA hybrids containing nonpolar pyrimidine isosteres defines regions essential for HIV type 1 polypurine tract selection. Proc Natl Acad Sci U S A (2003) 0.94
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Dynamic binding orientations direct activity of HIV reverse transcriptase. Nature (2008) 2.94
Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates. Science (2008) 2.78
A fluorescence-based high-throughput screening assay for inhibitors of human immunodeficiency virus-1 reverse transcriptase-associated ribonuclease H activity. Anal Biochem (2003) 1.87
Selective inhibition of HIV-1 reverse transcriptase-associated ribonuclease H activity by hydroxylated tropolones. Nucleic Acids Res (2005) 1.75
Altering the RNase H primer grip of human immunodeficiency virus reverse transcriptase modifies cleavage specificity. Biochemistry (2002) 1.64
A cis-acting element in retroviral genomic RNA links Gag-Pol ribosomal frameshifting to selective viral RNA encapsidation. Cell Host Microbe (2013) 1.56
Multimode, cooperative mechanism of action of allosteric HIV-1 integrase inhibitors. J Biol Chem (2012) 1.55
'Binding, bending and bonding': polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus. Int J Biochem Cell Biol (2004) 1.46
Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase. J Biol Chem (2002) 1.45
Identification of specific HIV-1 reverse transcriptase contacts to the viral RNA:tRNA complex by mass spectrometry and a primary amine selective reagent. Proc Natl Acad Sci U S A (2002) 1.26
An unusual topological structure of the HIV-1 Rev response element. Cell (2013) 1.26
Synthesis, activity, and structural analysis of novel α-hydroxytropolone inhibitors of human immunodeficiency virus reverse transcriptase-associated ribonuclease H. J Med Chem (2011) 1.24
Resistance to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response element. Proc Natl Acad Sci U S A (2008) 1.22
Dissecting APOBEC3G substrate specificity by nucleoside analog interference. J Biol Chem (2009) 1.17
Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription. Nat Struct Mol Biol (2010) 1.15
Mutations in the ribonuclease H active site of HIV-RT reveal a role for this site in stabilizing enzyme-primer-template binding. Biochemistry (2002) 1.15
Identification of an inhibitor-binding site to HIV-1 integrase with affinity acetylation and mass spectrometry. Proc Natl Acad Sci U S A (2004) 1.13
Multiple sources of contamination in samples from patients reported to have XMRV infection. PLoS One (2012) 1.08
Role of the Reverse Transcriptase, Nucleocapsid Protein, and Template Structure in the Two-step Transfer Mechanism in Retroviral Recombination. J Biol Chem (2003) 1.07
Mutations M184V and Y115F in HIV-1 reverse transcriptase discriminate against "nucleotide-competing reverse transcriptase inhibitors". J Biol Chem (2008) 1.06
The RNA transport element of the murine musD retrotransposon requires long-range intramolecular interactions for function. J Biol Chem (2010) 1.04
Structure-activity analysis of vinylogous urea inhibitors of human immunodeficiency virus-encoded ribonuclease H. Antimicrob Agents Chemother (2010) 1.03
Identifying and characterizing a functional HIV-1 reverse transcriptase-binding site on integrase. J Biol Chem (2009) 1.03
Correlating SHAPE signatures with three-dimensional RNA structures. RNA (2011) 1.03
A ribose sugar conformational switch in the LTR-retrotransposon Ty3 polypurine tract-containing RNA/DNA hybrid. J Am Chem Soc (2005) 0.98
Ty3 integrase is required for initiation of reverse transcription. J Virol (2002) 0.98
The xenotropic murine leukemia virus-related retrovirus debate continues at first international workshop. Retrovirology (2010) 0.98
High-resolution NMR analysis of the conformations of native and base analog substituted retroviral and LTR-retrotransposon PPT primers. Chem Biol (2008) 0.96
In-gel probing of individual RNA conformers within a mixed population reveals a dimerization structural switch in the HIV-1 leader. Nucleic Acids Res (2013) 0.96
Exploring Ty1 retrotransposon RNA structure within virus-like particles. Nucleic Acids Res (2012) 0.95
A dimeric lactone from Ardisia japonica with inhibitory activity for HIV-1 and HIV-2 ribonuclease H. J Nat Prod (2007) 0.95
SHAMS: combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids. RNA (2009) 0.95
Uncovering the complexities of retroviral ribonuclease H reveals its potential as a therapeutic target. AIDS Rev (2003) 0.95
Reverse transcriptase in motion: conformational dynamics of enzyme-substrate interactions. Biochim Biophys Acta (2009) 0.95
Nonpolar thymine isosteres in the Ty3 polypurine tract DNA template modulate processing and provide a model for its recognition by Ty3 reverse transcriptase. J Biol Chem (2003) 0.94
Hydrolysis of RNA/DNA hybrids containing nonpolar pyrimidine isosteres defines regions essential for HIV type 1 polypurine tract selection. Proc Natl Acad Sci U S A (2003) 0.94
Mass spectrometric analysis of the HIV-1 integrase-pyridoxal 5'-phosphate complex reveals a new binding site for a nucleotide inhibitor. J Biol Chem (2004) 0.94
Mutagenesis of human immunodeficiency virus reverse transcriptase p51 subunit defines residues contributing to vinylogous urea inhibition of ribonuclease H activity. J Biol Chem (2011) 0.94
Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands. Nucleic Acids Res (2008) 0.94
Direct and indirect contributions of RNA secondary structure elements to the initiation of HIV-1 reverse transcription. J Biol Chem (2002) 0.94
Functional interactions of nucleocapsid protein of feline immunodeficiency virus and cellular prion protein with the viral RNA. J Mol Biol (2002) 0.93
SHAPE analysis of the FIV Leader RNA reveals a structural switch potentially controlling viral packaging and genome dimerization. Nucleic Acids Res (2011) 0.93
Examining the role of the HIV-1 reverse transcriptase p51 subunit in positioning and hydrolysis of RNA/DNA hybrids. J Biol Chem (2013) 0.92
Human immunodeficiency virus type 2 reverse transcriptase activity in model systems that mimic steps in reverse transcription. J Virol (2003) 0.92
Nucleotide excision repair and template-independent addition by HIV-1 reverse transcriptase in the presence of nucleocapsid protein. J Biol Chem (2006) 0.91
Mutating conserved residues in the ribonuclease H domain of Ty3 reverse transcriptase affects specialized cleavage events. J Biol Chem (2002) 0.91
An HIV RNase H inhibitory 1,3,4,5-tetragalloylapiitol from the African plant Hylodendron gabunensis. J Nat Prod (2007) 0.91
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res (2013) 0.89
Purine analog substitution of the HIV-1 polypurine tract primer defines regions controlling initiation of plus-strand DNA synthesis. Nucleic Acids Res (2006) 0.89
Active site and allosteric inhibitors of the ribonuclease H activity of HIV reverse transcriptase. Future Med Chem (2013) 0.88
Examining interactions of HIV-1 reverse transcriptase with single-stranded template nucleotides by nucleoside analog interference. J Biol Chem (2006) 0.88
Structural complexity of Dengue virus untranslated regions: cis-acting RNA motifs and pseudoknot interactions modulating functionality of the viral genome. Nucleic Acids Res (2013) 0.88
A capillary electrophoretic assay for ribonuclease H activity. Anal Biochem (2004) 0.88
Two modes of HIV-1 polypurine tract cleavage are affected by introducing locked nucleic acid analogs into the (-) DNA template. J Biol Chem (2004) 0.86
Attenuation of DNA replication by HIV-1 reverse transcriptase near the central termination sequence. Biochemistry (2005) 0.86
Examining the ribonuclease H primer grip of HIV-1 reverse transcriptase by charge neutralization of RNA/DNA hybrids. Nucleic Acids Res (2008) 0.85
HIV-1 transmission by dendritic cell-specific ICAM-3-grabbing nonintegrin (DC-SIGN) is regulated by determinants in the carbohydrate recognition domain that are absent in liver/lymph node-SIGN (L-SIGN). J Biol Chem (2009) 0.85
Investigating HIV-1 polypurine tract geometry via targeted insertion of abasic lesions in the (-)-DNA template and (+)-RNA primer. J Biol Chem (2005) 0.84
Analysis of HIV-1 replication block due to substitutions at F61 residue of reverse transcriptase reveals additional defects involving the RNase H function. Nucleic Acids Res (2006) 0.84
HIV-1 ribonuclease H inhibitory phenolic glycosides from Eugenia hyemalis. J Nat Prod (2008) 0.82
Probing anomalous structural features in polypurine tract-containing RNA-DNA hybrids with neomycin B. Biochemistry (2009) 0.82
Exploiting structurally diverse nucleoside analogs as probes of reverse transcription complexes. Curr HIV Res (2007) 0.82
Identification of biologically active, HIV TAR RNA-binding small molecules using small molecule microarrays. J Am Chem Soc (2014) 0.81
Investigating the "steric gate" of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase by targeted insertion of unnatural amino acids. Biochemistry (2007) 0.81
Functional roles of carboxylate residues comprising the DNA polymerase active site triad of Ty3 reverse transcriptase. Nucleic Acids Res (2005) 0.81
Examining Ty3 polypurine tract structure and function by nucleoside analog interference. J Biol Chem (2005) 0.81
The HIV-2 Rev-response element: determining secondary structure and defining folding intermediates. Nucleic Acids Res (2013) 0.80
Revisiting plus-strand DNA synthesis in retroviruses and long terminal repeat retrotransposons: dynamics of enzyme: substrate interactions. Viruses (2009) 0.80
Interaction of the Ty3 reverse transcriptase thumb subdomain with template-primer. J Biol Chem (2005) 0.80
Exploiting drug-resistant enzymes as tools to identify thienopyrimidinone inhibitors of human immunodeficiency virus reverse transcriptase-associated ribonuclease H. J Med Chem (2013) 0.80
Site- and subunit-specific incorporation of unnatural amino acids into HIV-1 reverse transcriptase. Protein Expr Purif (2004) 0.80
Probing Retroviral and Retrotransposon Genome Structures: The "SHAPE" of Things to Come. Mol Biol Int (2012) 0.80
Basic quinolinonyl diketo acid derivatives as inhibitors of HIV integrase and their activity against RNase H function of reverse transcriptase. J Med Chem (2014) 0.80
Solid-Phase Synthesis of 5'-O-β,γ-Methylenetriphosphate Derivatives of Nucleosides and Evaluation of Their Inhibitory Activity Against HIV-1 Reverse Transcriptase. Tetrahedron Lett (2010) 0.79
Synthetic tRNALys,3 as the replication primer for the HIV-1HXB2 and HIV-1Mal genomes. Nucleic Acids Res (2004) 0.79
Influence of RNA structural elements on Ty1 retrotransposition. Mob Genet Elements (2013) 0.79
Viral reverse transcriptases show selective high affinity binding to DNA-DNA primer-templates that resemble the polypurine tract. PLoS One (2012) 0.78
Reply to "Structural requirements for RNA degradation by HIV-1 reverse transcriptase". Nat Struct Mol Biol (2013) 0.77
RNA secondary structure prediction using high-throughput SHAPE. J Vis Exp (2013) 0.77
Intrinsic DNA synthesis fidelity of xenotropic murine leukemia virus-related virus reverse transcriptase. FEBS J (2012) 0.76
Effects of tRNA 3 Lys aminoacylation on the initiation of HIV-1 reverse transcription. Biochimie (2003) 0.76
Insights into secondary and tertiary interactions of dengue virus RNA by SHAPE. Methods Mol Biol (2014) 0.76
Unraveling the gymnastics of reverse transcription through single molecule spectroscopy. AIDS Res Hum Retroviruses (2014) 0.75
Inhibition of multi-drug resistant HIV-1 reverse transcriptase by nucleoside β-triphosphates. Bioorg Med Chem Lett (2011) 0.75
Sesquiterpenoid tropolone glycosides from Liriosma ovata. J Nat Prod (2015) 0.75
New monoterpene glycosides and phenolic compounds from Distylium racemosum and their inhibitory activity against ribonuclease H. Bioorg Med Chem Lett (2011) 0.75