A novel strategy for the identification of protein-DNA contacts by photocrosslinking and mass spectrometry.

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Nucleic Acids Research

• Publication date

  Unknown publication date

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1093/NAR/GNH131PMID 15383647PMCID PMC519130
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A novel Gal(beta1-4)Gal(beta1-4)Fuc(alpha1-6)-core modification attached to the proximal N-acetylglucosamine of keyhole limpet haemocyanin (KLH) N-glycans.

  2004cited by this paper
• Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold.

  2004cited by this paper
• An optimized protocol for nano-LC-MALDI-TOF-MS coupling for the analysis of proteolytic digests of glycoproteins.

  2004cited by this paper
• PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes.

  2003cited by this paper
• The Synthesis of Teichoic Acids

  2003cited by this paper
• Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry.

  2002cited by this paper
• Evolutionary Relationship between Different Subgroups of Restriction Endonucleases*

  2002cited by this paper
• Mass spectrometric analysis of a UV‐cross‐linked protein–DNA complex: Tryptophans 54 and 88 of E. coli SSB cross‐link to DNA

  2001influential reference
• Metabotropic glutamate receptors: novel targets for pain relief

  2001cited by this paper
• Identification of the amino acid residues of the amino terminus of vimentin responsible for DNA binding by enzymatic and chemical sequencing and analysis by MALDI-TOF.

  2000cited by this paper
• Identification of a base-specific contact between the restriction endonuclease SsoII and its recognition sequence by photocross-linking.

  2000cited by this paper
• Identification of tyrosine 204 as the photo-cross-linking site in the DNA-EcoRI DNA methyltransferase complex by electrospray ionization mass spectrometry.

  2000cited by this paper
• Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA

  2000cited by this paper
• Electron capture dissociation of singly and multiply phosphorylated peptides.

  2000influential reference
• Characterization of a cross-linked DNA-Endonuclease VIII repair complex by electrospray ionization mass spectrometry

  2000cited by this paper
• Mass spectral characterization of a protein—nucleic acid photocrosslink

  1999cited by this paper
• Photocross-linking of the Homing Endonuclease PI-SceI to Its Recognition Sequence*

  1999cited by this paper
• Probing the interaction of T7 RNA polymerase with promoter.

  1999cited by this paper
• Identification of the Binding Site for the Extrahelical Target Base in N 6-Adenine DNA Methyltransferases by Photo-cross-linking with Duplex Oligodeoxyribonucleotides Containing 5-Iodouracil at the Target Position*

  1999cited by this paper
• An improved PCR-mutagenesis strategy for two-site mutagenesis or sequence swapping between related genes.

  1998cited by this paper
• Probing the Binding Region of the Single‐Stranded DNA‐Binding Domain of Rat DNA Polymerase β Using Nanosecond‐Pulse Laser‐Induced Cross‐Linking and Mass Spectrometry

  1998cited by this paper
• Structural Elucidation and Monokine-inducing Activity of Two Biologically Active Zwitterionic Glycosphingolipids Derived from the Porcine Parasitic Nematode Ascaris suum *

  1998cited by this paper
• Photocross-linking of nucleic acids to associated proteins.

  1997cited by this paper
• Identification and Sequence Analysis of Contact Sites between Ribosomal Proteins and rRNA in Escherichia coli 30 S Subunits by a New Approach Using Matrix-assisted Laser Desorption/Ionization-Mass Spectrometry Combined with N-terminal Microsequencing*

  1997cited by this paper
• Identification and characterization of posttranslational modifications of proteins by MALDI ion trap mass spectrometry.

  1997cited by this paper
• Characterization of peptide-oligonucleotide heteroconjugates by mass spectrometry.

  1996cited by this paper
• Mechanistic Studies of the 5-Iodouracil Chromophore Relevant to Its Use in Nucleoprotein Photo-Cross-Linking

  1996cited by this paper
• Inhibitory DNA ligands to platelet-derived growth factor B-chain.

  1996cited by this paper
• Differential proximity probing of two DNA binding sites in the Escherichia coli recA protein using photo-cross-linking methods.

  1996cited by this paper
• Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution.

  1996cited by this paper
• Photocross-links between Single-stranded DNA and Escherichia coli RecA Protein Map to Loops L1 (Amino Acid Residues 157-164) and L2 (Amino Acid Residues 195-209) (*)

  1995cited by this paper
• Protein‐rRNA binding features and their structural and functional implications in ribosomes as determined by cross‐linking studies.

  1995cited by this paper
• Photocrosslinking of 5-iodouracil-substituted RNA and DNA to proteins.

  1993cited by this paper
• Identification of residues in the single-stranded DNA-binding site of the 8-kDa domain of rat DNA polymerase beta by UV cross-linking.

  1993cited by this paper
• Direct observation of UV-crosslinked protein-nucleic acid complexes by matrix-assisted laser desorption ionization mass spectrometry.

  1993cited by this paper
• Identification of amino acids in lac repressor protein cross-linked to operator DNA specifically substituted with bromodeoxyuridine.

  1991cited by this paper
• Glycosphingolipids in insects. Chemical structures of two variants of a glucuronic-acid-containing ceramide hexasaccharide from a pupae of Calliphora vicina (Insecta: Diptera), distinguished by a N-acetylglucosamine-bound phosphoethanolamine sidechain.

  1990cited by this paper
• Structural analysis of the glycosylinositol phospholipid anchors of membrane proteins

  1990cited by this paper
• Contributions of mass spectrometry to peptide and protein structure.

  1988influential reference
• Glycosyl-phosphatidylinositol moiety that anchors Trypanosoma brucei variant surface glycoprotein to the membrane.

  1988cited by this paper
• Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography.

  1986cited by this paper
• Glycosphingolipids in insects. Chemical structures of ceramide monosaccharide, disaccharide, and trisaccharide from pupae of Calliphora vicina (Insecta: Diptera).

  1985cited by this paper
• Photochemical cross-linking of the Escherichia coli single-stranded DNA-binding protein to oligodeoxynucleotides. Identification of phenylalanine 60 as the site of cross-linking.

  1984cited by this paper
• Proposal for a common nomenclature for sequence ions in mass spectra of peptides.

  1984cited by this paper
• Glycerophosphoryl diglucosyl diglyceride, a new phosphoglycolipid from Streptococci.

  1973cited by this paper
• The lipid-teichoic acid complex in the cytoplasmic membrane of Streptococcus faecalis N.C.I.B. 8191.

  1972cited by this paper
• The structure of a glycerylphosphoryldiglucosyl diglyceride from the lipids of Acholeplasma laidlawii strain B.

  1972cited by this paper
• THE SYNTHESIS OF TEICHOIC ACIDS. 3. GLUCOSYLATION OF POLYGLYCEROPHOSPHATE.

  1964cited by this paper
• The Iodination of Nucleosides and Nucleotides

  1963cited by this paper

• JEDII: Juxtaposition Enabled DNA-binding Interface Identifier

  2022cites this paper
• Mass Spectrometry of Nucleic Acid Noncovalent Complexes.

  2021cites this paper
• Synthesis and Characterization of Site‐Specific O6‐Alkylguanine DNA‐Alkyl Transferase‐Oligonucleotide Crosslinks

  2019cites this paper
• Identification of proximal sites for unwound DNA substrate in E . coli topoisomerase I with oxidative crosslinking

  2017cites this paper
• Identification of proximal sites for unwound DNA substrate in Escherichia coli topoisomerase I with oxidative crosslinking

  2017cites this paper
• Application of Mass Spectrometry in Biology and Physiology

  2016cites this paper
• Applying mass spectrometry to study non-covalent biomolecule complexes.

  2016cites this paper
• Applying MALDI-ToF mass spectrometry to study non-covalent interactions

  2014cites this paper
• Synthesis of Light-Activated Nucleotides and Unnatural Amino Acids for Biological Applications

  2013cites this paper
• MALDI-ToF mass spectrometry for studying noncovalent complexes of biomolecules.

  2013cites this paper
• Investigation of protein-RNA interactions by UV cross-linking and mass spectrometry: Methodological improvements toward in vivo applications.

  2013influential citation
• Investigation of protein-RNA interactions by mass spectrometry--Techniques and applications.

  2012influential citation
• Virus Adaptation and Treatment Mapping protein – RNA interactions

  2012cites this paper
• Mapping protein–RNA interactions

  2012cites this paper
• Mass-spectrometric analysis of proteins cross-linked to 4-thio-uracil- and 5-bromo-uracil-substituted RNA.

  2011cites this paper
• Genetically encoding an aliphatic diazirine for protein photocrosslinking

  2011cites this paper
• Analysis of RNA: Peptide heteroconjugates by electron induced dissociation mass spectrometry

  2011cites this paper
• Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry

  2010cites this paper
• From an electrophoretic mobility shift assay to isolated transcription factors: a fast genomic-proteomic approach

  2010cites this paper
• A eole for the MS analysis of nucleic acids in the post-genomics age

  2010cites this paper
• Sequence analysis of peptide:oligonucleotide heteroconjugates by electron capture dissociation and electron transfer dissociation

  2010cites this paper
• Enrichment of protein-RNA crosslinks from crude UV-irradiated mixtures for MS analysis by on-line chromatography using titanium dioxide columns.

  2009cites this paper
• Method for the affinity purification of covalently linked peptides following cyanogen bromide cleavage of proteins.

  2009cites this paper
• Genetic and Biochemical Properties of Arabidopsis RNA Polymerases IV and V

  2009cites this paper
• Light as a Tool for Biologists: Recent Developments

  2008cites this paper
• Enzyme-dependent Variations in the Polysialylation of the Neural Cell Adhesion Molecule (NCAM) in Vivo*

  2008cites this paper
• Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies.

  2008cites this paper
• MALDI‐MS of Nucleic Acids and Practical Implementations in Genomics and Genetics

  2007cites this paper
• Detection of protein-RNA crosslinks by nanoLC-ESI-MS/MS using precursor ion scanning and multiple reaction monitoring (MRM) experiments

  2007cites this paper
• Improved identification of enriched peptide–RNA cross-links from ribonucleoprotein particles (RNPs) by mass spectrometry

  2007cites this paper
• A Simple and Efficient Photoaffinity Method for Proteomics of GTP‐Binding Proteins

  2007cites this paper
• Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing.

  2006cites this paper
• Predicting DNA-binding sites of proteins from amino acid sequence

  2006cites this paper
• Juzen-taiho-to (Shi-Quan-Da-Bu-Tang): Scientific Evaluation and Clinical Application

  2006cites this paper
• Photoaffinity labeling combined with mass spectrometric approaches as a tool for structural proteomics

  2006cites this paper
• Structural characterization of metal and DNA binding to DREAM protein, a calcium sensing transcriptional repressor in pain modulation

  2006cites this paper
• Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII.

  2005cites this paper
• Current literature in mass spectrometry.

  2005cites this paper
• Specificity Changes in the Evolution of Type II Restriction Endonucleases

  2005cites this paper
• Complete MALDI-ToF MS analysis of cross-linked peptide-RNA oligonucleotides derived from nonlabeled UV-irradiated ribonucleoprotein particles.

  2005cites this paper
• Identific ation of interface residues involved in protein-protein and protein-DNA interactions from sequence using machine learning approaches

  2005cites this paper