Published in J Am Chem Soc on September 19, 2007
Determining the specificity of protein-DNA interactions. Nat Rev Genet (2010) 2.38
High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display. Nucleic Acids Res (2009) 1.43
Specificity landscapes of DNA binding molecules elucidate biological function. Proc Natl Acad Sci U S A (2010) 1.39
All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues. BMC Genomics (2008) 1.28
Next generation hairpin polyamides with (R)-3,4-diaminobutyric acid turn unit. J Am Chem Soc (2008) 1.23
Efficiency, error and yield in light-directed maskless synthesis of DNA microarrays. J Nanobiotechnology (2011) 1.07
In vivo imaging of pyrrole-imidazole polyamides with positron emission tomography. Proc Natl Acad Sci U S A (2008) 1.07
A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity. Nucleic Acids Res (2011) 0.97
Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J Am Chem Soc (2012) 0.97
CSI-FID: high throughput label-free detection of DNA binding molecules. Bioorg Med Chem Lett (2009) 0.96
CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data. Nucleic Acids Res (2008) 0.88
Quantitative detection of small molecule/DNA complexes employing a force-based and label-free DNA-microarray. Biophys J (2009) 0.87
Mapping polyamide-DNA interactions in human cells reveals a new design strategy for effective targeting of genomic sites. Angew Chem Int Ed Engl (2014) 0.82
Melting thermodynamics of reversible DNA/ligand complexes at interfaces. J Am Chem Soc (2012) 0.81
An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example. PLoS One (2013) 0.81
Small-molecule regulators that mimic transcription factors. Biochim Biophys Acta (2010) 0.80
Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing. Nucleic Acids Res (2016) 0.77
Dry and wet approaches for genome-wide functional annotation of conventional and unconventional transcriptional activators. Comput Struct Biotechnol J (2016) 0.77
Combinatorial bZIP dimers display complex DNA-binding specificity landscapes. Elife (2017) 0.77
Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes. Brief Funct Genomics (2014) 0.76
Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin). J Vis Exp (2016) 0.75
Sliding on DNA: From Peptides to Small Molecules. Angew Chem Int Ed Engl (2016) 0.75
Characterization of self-assembled DNA concatemers from synthetic oligonucleotides. Comput Struct Biotechnol J (2014) 0.75
Identification of novel peptoid agonists of fibroblast growth factor receptor using microarray-based screening. Medchemcomm (2016) 0.75
Mapping the affinity landscape of Thrombin-binding aptamers on 2'F-ANA/DNA chimeric G-Quadruplex microarrays. Nucleic Acids Res (2017) 0.75
Efficient Synthesis of Peptide and Protein Functionalized Pyrrole-Imidazole Polyamides Using Native Chemical Ligation. Int J Mol Sci (2015) 0.75
Synthetic genome readers target clustered binding sites across diverse chromatin states. Proc Natl Acad Sci U S A (2016) 0.75
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Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol (1999) 9.35
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A (2001) 5.08
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03
Recognition of the DNA minor groove by pyrrole-imidazole polyamides. Curr Opin Struct Biol (2003) 3.80
Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci U S A (2006) 2.97
SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis. Bioinformatics (2002) 2.69
Echinomycin, a small-molecule inhibitor of hypoxia-inducible factor-1 DNA-binding activity. Cancer Res (2005) 2.49
Echinomycin binding sites on DNA. Science (1984) 2.44
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Inhibition of vascular endothelial growth factor with a sequence-specific hypoxia response element antagonist. Proc Natl Acad Sci U S A (2004) 2.25
Footprinting methods for analysis of pyrrole-imidazole polyamide/DNA complexes. Methods Enzymol (2001) 1.97
DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA.TTC repeats in Friedreich's ataxia. Proc Natl Acad Sci U S A (2006) 1.70
A fluorescent intercalator displacement assay for establishing DNA binding selectivity and affinity. Acc Chem Res (2004) 1.59
Completion of a Programmable DNA-Binding Small Molecule Library. Tetrahedron (2007) 1.58
Improved nuclear localization of DNA-binding polyamides. Nucleic Acids Res (2006) 1.55
Shape selective recognition of T.A base pairs by hairpin polyamides containing N-terminal 3-methoxy (and 3-chloro) thiophene residues. Bioorg Med Chem (2003) 1.10
Toward rules for 1:1 polyamide:DNA recognition. Proc Natl Acad Sci U S A (2001) 1.07
Programmable oligomers for minor groove DNA recognition. J Am Chem Soc (2006) 1.06
Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays. Methods Enzymol (2006) 1.02
Structure of a beta-alanine-linked polyamide bound to a full helical turn of purine tract DNA in the 1:1 motif. J Mol Biol (2002) 1.01
Expanding the repertoire of heterocycle ring pairs for programmable minor groove DNA recognition. J Am Chem Soc (2004) 0.86
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell (2008) 4.49
Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell (2006) 3.46
Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci U S A (2006) 2.97
TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II. Mol Cell (2009) 2.61
Gene loops enhance transcriptional directionality. Science (2012) 2.50
Regulator trafficking on bacterial transcription units in vivo. Mol Cell (2009) 2.43
A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell (2004) 2.27
Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex. Mol Cell Biol (2004) 2.26
Inhibition of vascular endothelial growth factor with a sequence-specific hypoxia response element antagonist. Proc Natl Acad Sci U S A (2004) 2.25
Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J Bacteriol (2005) 2.06
Suppression of androgen receptor-mediated gene expression by a sequence-specific DNA-binding polyamide. Proc Natl Acad Sci U S A (2007) 2.04
Arresting cancer proliferation by small-molecule gene regulation. Chem Biol (2004) 1.90
Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates. Nucleic Acids Res (2004) 1.84
Modulating hypoxia-inducible transcription by disrupting the HIF-1-DNA interface. ACS Chem Biol (2007) 1.84
Accessibility of nuclear chromatin by DNA binding polyamides. Chem Biol (2003) 1.81
Nuclear localization of pyrrole-imidazole polyamide-fluorescein conjugates in cell culture. Proc Natl Acad Sci U S A (2003) 1.80
Chemical-genomic dissection of the CTD code. Nat Struct Mol Biol (2010) 1.76
Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis. Proc Natl Acad Sci U S A (2007) 1.71
DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA.TTC repeats in Friedreich's ataxia. Proc Natl Acad Sci U S A (2006) 1.70
Polyamides reveal a role for repression in latency within resting T cells of HIV-infected donors. J Infect Dis (2004) 1.64
Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands. J Mol Biol (2003) 1.63
Allosteric modulation of DNA by small molecules. Proc Natl Acad Sci U S A (2009) 1.61
Completion of a Programmable DNA-Binding Small Molecule Library. Tetrahedron (2007) 1.58
Improved nuclear localization of DNA-binding polyamides. Nucleic Acids Res (2006) 1.55
Cellular uptake of N-methylpyrrole/N-methylimidazole polyamide-dye conjugates. Bioorg Med Chem (2002) 1.52
Fingers reach for the genome. Nat Biotechnol (2003) 1.48
Solid-phase synthesis of DNA binding polyamides on oxime resin. Bioorg Med Chem (2002) 1.45
Specificity landscapes of DNA binding molecules elucidate biological function. Proc Natl Acad Sci U S A (2010) 1.39
Repression of DNA-binding dependent glucocorticoid receptor-mediated gene expression. Proc Natl Acad Sci U S A (2009) 1.38
Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders. Proc Natl Acad Sci U S A (2011) 1.36
Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo. Mol Cell (2005) 1.32
Ssu72 phosphatase-dependent erasure of phospho-Ser7 marks on the RNA polymerase II C-terminal domain is essential for viability and transcription termination. J Biol Chem (2012) 1.30
A TAD further: exogenous control of gene activation. ACS Chem Biol (2007) 1.27
Molecular recognition of the nucleosomal "supergroove". Proc Natl Acad Sci U S A (2004) 1.25
Targeted derepression of the human immunodeficiency virus type 1 long terminal repeat by pyrrole-imidazole polyamides. J Virol (2002) 1.24
Next generation hairpin polyamides with (R)-3,4-diaminobutyric acid turn unit. J Am Chem Soc (2008) 1.23
Cooperativity in RNA-protein interactions: global analysis of RNA binding specificity. Cell Rep (2012) 1.22
Cyclic pyrrole-imidazole polyamides targeted to the androgen response element. J Am Chem Soc (2009) 1.21
Structural basis for cyclic Py-Im polyamide allosteric inhibition of nuclear receptor binding. J Am Chem Soc (2010) 1.15
Antitumor activity of a pyrrole-imidazole polyamide. Proc Natl Acad Sci U S A (2013) 1.13
The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin. Genes Dev (2010) 1.11
Sequence specific fluorescence detection of double strand DNA. J Am Chem Soc (2003) 1.11
Blocking transcription through a nucleosome with synthetic DNA ligands. J Mol Biol (2002) 1.11
Shape selective recognition of T.A base pairs by hairpin polyamides containing N-terminal 3-methoxy (and 3-chloro) thiophene residues. Bioorg Med Chem (2003) 1.10
Small molecule transcription factor mimic. J Am Chem Soc (2004) 1.10
Design of artificial transcriptional activators with rigid poly-L-proline linkers. J Am Chem Soc (2002) 1.09
Role of mismatch repair enzymes in GAA·TTC triplet-repeat expansion in Friedreich ataxia induced pluripotent stem cells. J Biol Chem (2012) 1.09
Quantitating the concentration of Py-Im polyamide-fluorescein conjugates in live cells. Bioorg Med Chem Lett (2008) 1.08
The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally. PLoS Genet (2013) 1.08
Emerging Views on the CTD Code. Genet Res Int (2012) 1.08
In vivo imaging of pyrrole-imidazole polyamides with positron emission tomography. Proc Natl Acad Sci U S A (2008) 1.07
DNA-templated dimerization of hairpin polyamides. J Am Chem Soc (2003) 1.07
Targeted chemical wedges reveal the role of allosteric DNA modulation in protein-DNA assembly. ACS Chem Biol (2008) 1.06
Programmable oligomers for minor groove DNA recognition. J Am Chem Soc (2006) 1.06
Matrix metalloproteinase-9 genotype as a potential genetic marker for abdominal aortic aneurysm. Circ Cardiovasc Genet (2012) 1.05
Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide. Proc Natl Acad Sci U S A (2012) 1.04
Pharmacokinetics of Py-Im polyamides depend on architecture: cyclic versus linear. J Am Chem Soc (2012) 1.03
Toward artificial developmental regulators. J Am Chem Soc (2003) 1.02
Addressing single molecules on DNA nanostructures. Angew Chem Int Ed Engl (2007) 1.02
Sequence-specific fluorescence detection of DNA by polyamide-thiazole orange conjugates. J Am Chem Soc (2005) 1.02
DNA crosslinking and biological activity of a hairpin polyamide-chlorambucil conjugate. Nucleic Acids Res (2003) 1.01
Structure of a beta-alanine-linked polyamide bound to a full helical turn of purine tract DNA in the 1:1 motif. J Mol Biol (2002) 1.01
Imidazopyridine/Pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition. J Am Chem Soc (2003) 1.01
NMR structure of a cyclic polyamide-DNA complex. J Am Chem Soc (2004) 0.99
The origin recognition complex interacts with a subset of metabolic genes tightly linked to origins of replication. PLoS Genet (2009) 0.98
Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus. Proc Natl Acad Sci U S A (2013) 0.98
Nucleosomes in solution exist as a mixture of twist-defect states. J Mol Biol (2005) 0.98
Microwave assisted synthesis of Py-Im polyamides. Org Lett (2012) 0.98
Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J Am Chem Soc (2012) 0.97
RNA sequences that work as transcriptional activating regions. Nucleic Acids Res (2003) 0.97
Minimization of a protein-DNA dimerizer. J Am Chem Soc (2007) 0.97
Inhibition of DNA binding by NF-kappa B with pyrrole-imidazole polyamides. Biochemistry (2002) 0.97
Single-dose pharmacokinetic and toxicity analysis of pyrrole-imidazole polyamides in mice. Cancer Chemother Pharmacol (2012) 0.97
Jarid2 (Jumonji, AT rich interactive domain 2) regulates NOTCH1 expression via histone modification in the developing heart. J Biol Chem (2011) 0.96
Characterization and solubilization of pyrrole-imidazole polyamide aggregates. J Med Chem (2012) 0.96
Allosteric inhibition of zinc-finger binding in the major groove of DNA by minor-groove binding ligands. Biochemistry (2004) 0.96
Design of a sequence-specific DNA bisintercalator. Angew Chem Int Ed Engl (2004) 0.96
CSI-FID: high throughput label-free detection of DNA binding molecules. Bioorg Med Chem Lett (2009) 0.96
Allosteric inhibition of protein--DNA complexes by polyamide--intercalator conjugates. J Am Chem Soc (2003) 0.96
Promoter scanning for transcription inhibition with DNA-binding polyamides. Mol Cell Biol (2002) 0.96
A two-hit mechanism for pre-mitotic arrest of cancer cell proliferation by a polyamide-alkylator conjugate. Cell Cycle (2006) 0.94
Unanticipated differences between alpha- and gamma-diaminobutyric acid-linked hairpin polyamide-alkylator conjugates. Nucleic Acids Res (2006) 0.94
Enhancing the cellular uptake of Py-Im polyamides through next-generation aryl turns. Nucleic Acids Res (2011) 0.93
Fluorescent sequence-specific dsDNA binding oligomers. J Am Chem Soc (2007) 0.93
Alpha-diaminobutyric acid-linked hairpin polyamides. Bioorg Med Chem (2007) 0.92
Activity of a Py-Im polyamide targeted to the estrogen response element. Mol Cancer Ther (2013) 0.92
Temperature-sensitive protein-DNA dimerizers. Proc Natl Acad Sci U S A (2005) 0.92