Published in J Am Chem Soc on November 29, 2011
QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. RNA (2012) 1.60
The mechanisms of RNA SHAPE chemistry. J Am Chem Soc (2012) 1.52
Moloney murine leukemia virus glyco-gag facilitates xenotropic murine leukemia virus-related virus replication through human APOBEC3-independent mechanisms. Retrovirology (2012) 0.88
Incorporating global features of RNA motifs in predictions for an ensemble of secondary structures for encapsidated MS2 bacteriophage RNA. RNA (2012) 0.86
Global RNA structure analysis of poliovirus identifies a conserved RNA structure involved in viral replication and infectivity. J Virol (2013) 0.81
Probing Retroviral and Retrotransposon Genome Structures: The "SHAPE" of Things to Come. Mol Biol Int (2012) 0.80
An immature retroviral RNA genome resembles a kinetically trapped intermediate state. J Virol (2014) 0.80
Human and murine APOBEC3s restrict replication of koala retrovirus by different mechanisms. Retrovirology (2015) 0.75
Retracted Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome. Science (2009) 10.76
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 10.35
Retracted Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PLoS Pathog (2006) 10.08
RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc (2005) 6.46
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc (2006) 6.14
Architecture and secondary structure of an entire HIV-1 RNA genome. Nature (2009) 6.12
Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci U S A (2008) 5.44
A new human prostate carcinoma cell line, 22Rv1. In Vitro Cell Dev Biol Anim (1999) 4.93
Identification of a signal in a murine retrovirus that is sufficient for packaging of nonretroviral RNA into virions. J Virol (1988) 4.88
A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J Am Chem Soc (2007) 4.81
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol (2008) 4.40
Recombinant origin of the retrovirus XMRV. Science (2011) 3.54
Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A (2011) 3.30
How retroviruses select their genomes. Nat Rev Microbiol (2005) 2.99
Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. Prog Nucleic Acid Res Mol Biol (2005) 2.98
SHAPE-directed RNA secondary structure prediction. Methods (2010) 2.40
Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA. J Am Chem Soc (2008) 2.26
RNA flexibility in the dimerization domain of a gamma retrovirus. Nat Chem Biol (2005) 2.19
DNA sequencing with chain-terminating inhibitors. 1977. Biotechnology (1992) 2.13
Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus. Nature (2004) 2.05
Analysis and localization of cyclophilin A found in the virions of human immunodeficiency virus type 1 MN strain. AIDS Res Hum Retroviruses (1995) 2.01
A cautionary tale of virus and disease. BMC Biol (2010) 1.93
Exploring RNA structural codes with SHAPE chemistry. Acc Chem Res (2011) 1.78
Laser-micropipet combination for single-cell analysis. Anal Chem (1998) 1.65
Architecture of a gamma retroviral genomic RNA dimer. Biochemistry (2006) 1.64
Time-resolved RNA SHAPE chemistry. J Am Chem Soc (2008) 1.48
Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome. Proc Natl Acad Sci U S A (2010) 1.46
Structure of an RNA switch that enforces stringent retroviral genomic RNA dimerization. Proc Natl Acad Sci U S A (2006) 1.43
Design considerations and effects of LNA in PCR primers. Mol Cell Probes (2003) 1.39
Chemical analysis of single cells. Annu Rev Anal Chem (Palo Alto Calif) (2008) 1.18
The SL1-SL2 (stem-loop) domain is the primary determinant for stability of the gamma retroviral genomic RNA dimer. J Biol Chem (2006) 1.11
Secondary structure of the mature ex virio Moloney murine leukemia virus genomic RNA dimerization domain. J Virol (2009) 1.09
Bipartite signal for genomic RNA dimerization in Moloney murine leukemia virus. J Virol (2002) 1.05
Critical review of recent developments in fluorescence detection for capillary electrophoresis. Electrophoresis (1997) 0.92
LNA-modified primers drastically improve hybridization to target RNA and reverse transcription. Biochemistry (2009) 0.90
RNA structure probing dash seq. Proc Natl Acad Sci U S A (2011) 0.89
Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers. Nucleic Acids Res (2006) 0.86
RNA structure: new messages in translation, replication and disease. Workshop on the role of RNA structures in the translation of viral and cellular RNAs. EMBO Rep (2009) 0.80
RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc (2005) 6.46
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc (2006) 6.14
Architecture and secondary structure of an entire HIV-1 RNA genome. Nature (2009) 6.12
Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci U S A (2008) 5.44
Endocytosis of HIV-1 activates plasmacytoid dendritic cells via Toll-like receptor-viral RNA interactions. J Clin Invest (2005) 5.00
A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J Am Chem Soc (2007) 4.81
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol (2008) 4.40
Analysis of single mammalian cells on-chip. Lab Chip (2007) 3.03
Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) is incorporated into HIV-1 virions through interactions with viral and nonviral RNAs. J Biol Chem (2004) 3.01
Human immunodeficiency virus type 1 cDNAs produced in the presence of APOBEC3G exhibit defects in plus-strand DNA transfer and integration. J Virol (2007) 2.95
RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts. J Am Chem Soc (2005) 2.92
SHAPE-directed RNA secondary structure prediction. Methods (2010) 2.40
Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA. J Am Chem Soc (2008) 2.26
RNA flexibility in the dimerization domain of a gamma retrovirus. Nat Chem Biol (2005) 2.19
Microfluidic devices for the high-throughput chemical analysis of cells. Anal Chem (2003) 2.14
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. Proc Natl Acad Sci U S A (2013) 2.11
Amino acid substitutions in Gag protein at non-cleavage sites are indispensable for the development of a high multitude of HIV-1 resistance against protease inhibitors. J Biol Chem (2001) 1.91
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
Photoresist with low fluorescence for bioanalytical applications. Anal Chem (2007) 1.81
Collection and expansion of single cells and colonies released from a micropallet array. Anal Chem (2007) 1.81
Micropallet arrays for the separation of single, adherent cells. Anal Chem (2007) 1.80
The interaction of APOBEC3G with human immunodeficiency virus type 1 nucleocapsid inhibits tRNA3Lys annealing to viral RNA. J Virol (2007) 1.74
Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA. RNA (2009) 1.68
Architecture of a gamma retroviral genomic RNA dimer. Biochemistry (2006) 1.64
On the significance of an RNA tertiary structure prediction. RNA (2010) 1.61
Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution. Nat Protoc (2009) 1.60
QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. RNA (2012) 1.60
Efficiency of human immunodeficiency virus type 1 postentry infection processes: evidence against disproportionate numbers of defective virions. J Virol (2007) 1.59
Micropatterning of living cells on a heterogeneously wetted surface. Langmuir (2006) 1.58
Micro total analysis systems for cell biology and biochemical assays. Anal Chem (2011) 1.58
Complex ligand-induced conformational changes in tRNA(Asp) revealed by single-nucleotide resolution SHAPE chemistry. Biochemistry (2008) 1.55
Nucleocapsid protein function in early infection processes. Virus Res (2008) 1.53
Broadening cell selection criteria with micropallet arrays of adherent cells. Cytometry A (2007) 1.52
The mechanisms of RNA SHAPE chemistry. J Am Chem Soc (2012) 1.52
SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA. Biochemistry (2008) 1.51
Interactions of murine APOBEC3 and human APOBEC3G with murine leukemia viruses. J Virol (2008) 1.50
Mechanistic insights into the kinetics of HIV-1 nucleocapsid protein-facilitated tRNA annealing to the primer binding site. J Mol Biol (2004) 1.49
Time-resolved RNA SHAPE chemistry. J Am Chem Soc (2008) 1.48
Human immunodeficiency virus type 1 nucleocapsid zinc-finger mutations cause defects in reverse transcription and integration. Virology (2006) 1.48
Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins. Nucleic Acids Res (2006) 1.47
Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides. Nucleic Acids Res (2006) 1.47
Trapping cells on a stretchable microwell array for single-cell analysis. Anal Bioanal Chem (2011) 1.47
Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome. Proc Natl Acad Sci U S A (2010) 1.46
Structure of an RNA switch that enforces stringent retroviral genomic RNA dimerization. Proc Natl Acad Sci U S A (2006) 1.43
Specific zinc-finger architecture required for HIV-1 nucleocapsid protein's nucleic acid chaperone function. Proc Natl Acad Sci U S A (2002) 1.42
Subtle alterations of the native zinc finger structures have dramatic effects on the nucleic acid chaperone activity of human immunodeficiency virus type 1 nucleocapsid protein. J Virol (2002) 1.39
High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly. Methods Enzymol (2009) 1.38
The cellular environment stabilizes adenine riboswitch RNA structure. Biochemistry (2013) 1.38
Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes. Nucleic Acids Res (2013) 1.37
Slow conformational dynamics at C2'-endo nucleotides in RNA. J Am Chem Soc (2008) 1.35
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc (2009) 1.33
Rapid kinetics of protein-nucleic acid interaction is a major component of HIV-1 nucleocapsid protein's nucleic acid chaperone function. J Mol Biol (2006) 1.32
Benchtop micromolding of polystyrene by soft lithography. Lab Chip (2011) 1.31
Genomic HIV RNA induces innate immune responses through RIG-I-dependent sensing of secondary-structured RNA. PLoS One (2012) 1.30
Examination of laser microbeam cell lysis in a PDMS microfluidic channel using time-resolved imaging. Lab Chip (2008) 1.26
Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs. RNA (2008) 1.25
Retroviral nucleocapsid proteins display nonequivalent levels of nucleic acid chaperone activity. J Virol (2008) 1.24
Real-time PCR analysis of HIV-1 replication post-entry events. Methods Mol Biol (2009) 1.22
Noninfectious papilloma virus-like particles inhibit HIV-1 replication: implications for immune control of HIV-1 infection by IL-27. Blood (2006) 1.21
Elimination of protease activity restores efficient virion production to a human immunodeficiency virus type 1 nucleocapsid deletion mutant. J Virol (2003) 1.21
Sharing and archiving nucleic acid structure mapping data. RNA (2011) 1.20
Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods (2012) 1.20
Mutational analysis of the C-terminal gag cleavage sites in human immunodeficiency virus type 1. J Virol (2007) 1.18
Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J Am Chem Soc (2012) 1.18
Chemical analysis of single cells. Annu Rev Anal Chem (Palo Alto Calif) (2008) 1.18
Two distinct binding modes of a protein cofactor with its target RNA. J Mol Biol (2006) 1.17
Laser-induced mixing in microfluidic channels. Anal Chem (2007) 1.16
Structural determinants of HIV-1 nucleocapsid protein for cTAR DNA binding and destabilization, and correlation with inhibition of self-primed DNA synthesis. J Mol Biol (2005) 1.16
Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry (2013) 1.16
Recruitment of intron-encoded and co-opted proteins in splicing of the bI3 group I intron RNA. Proc Natl Acad Sci U S A (2002) 1.16
C2'-endo nucleotides as molecular timers suggested by the folding of an RNA domain. Proc Natl Acad Sci U S A (2009) 1.16
Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry (2010) 1.13
Sorting and expansion of murine embryonic stem cell colonies using micropallet arrays. Cytometry A (2009) 1.13
The SL1-SL2 (stem-loop) domain is the primary determinant for stability of the gamma retroviral genomic RNA dimer. J Biol Chem (2006) 1.11
SHAPE-directed discovery of potent shRNA inhibitors of HIV-1. Mol Ther (2012) 1.11
Secondary structure of the mature ex virio Moloney murine leukemia virus genomic RNA dimerization domain. J Virol (2009) 1.09
Myristoyl-based transport of peptides into living cells. Biochemistry (2007) 1.09
Features, processing states, and heterologous protein interactions in the modulation of the retroviral nucleocapsid protein function. RNA Biol (2010) 1.08
Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs. PLoS Pathog (2013) 1.08
Isolation and manipulation of living adherent cells by micromolded magnetic rafts. Biomicrofluidics (2011) 1.08
Dimeric RNA recognition regulates HIV-1 genome packaging. PLoS Pathog (2013) 1.07
Simple photografting method to chemically modify and micropattern the surface of SU-8 photoresist. Langmuir (2006) 1.07
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
Surface-directed, graft polymerization within microfluidic channels. Anal Chem (2004) 1.07
Near native structure in an RNA collapsed state. Biochemistry (2003) 1.06
Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease. J Am Chem Soc (2010) 1.06
Mutations in human immunodeficiency virus type 1 nucleocapsid protein zinc fingers cause premature reverse transcription. J Virol (2008) 1.05
Structure-independent and quantitative ligation of single-stranded DNA. Anal Biochem (2005) 1.04
Differing roles of the N- and C-terminal zinc fingers in human immunodeficiency virus nucleocapsid protein-enhanced nucleic acid annealing. J Biol Chem (2003) 1.04
A guanosine-centric mechanism for RNA chaperone function. Science (2013) 1.03
Cofactors for human immunodeficiency virus type 1 cDNA integration in vitro. J Virol (2003) 1.03
Ribosome RNA assembly intermediates visualized in living cells. Biochemistry (2014) 1.03