9 results match your criteria resolving cross-link

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Mechanisms of Vertebrate DNA Interstrand Cross-Link Repair.

Annu Rev Biochem 2021 Jun 21;90:107-135. Epub 2021 Apr 21.

Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; email:

DNA interstrand cross-links (ICLs) covalently connect the two strands of the double helix and are extremely cytotoxic. Defective ICL repair causes the bone marrow failure and cancer predisposition syndrome, Fanconi anemia, and upregulation of repair causes chemotherapy resistance in cancer. The central event in ICL repair involves resolving the cross-link (unhooking). Read More

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Structural mechanism of DNA interstrand cross-link unhooking by the bacterial FAN1 nuclease.

J Biol Chem 2018 04 7;293(17):6482-6496. Epub 2018 Mar 7.

From the Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea,

DNA interstrand cross-links (ICLs) block the progress of the replication and transcription machineries and can weaken chromosomal stability, resulting in various diseases. FANCD2-FANCI-associated nuclease (FAN1) is a conserved structure-specific nuclease that unhooks DNA ICLs independently of the Fanconi anemia pathway. Recent structural studies have proposed two different mechanistic features for ICL unhooking by human FAN1: a specific basic pocket that recognizes the terminal phosphate of a 1-nucleotide (nt) 5' flap or FAN1 dimerization. Read More

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Cathepsin-L and transglutaminase dependent processing of ps20: A novel mechanism for ps20 regulation via ECM cross-linking.

Biochem Biophys Rep 2016 Sep 15;7:328-337. Epub 2016 Jun 15.

Department of Infectious Diseases, King's College London, United Kingdom.

Whey-acidic-protein (WAP) four-disulphide core (WFDC) proteins have important roles in the regulation of innate immunity, anti-microbial function, and the inhibition of inflammatory proteases at mucosal surfaces. It was recently demonstrated that the WFDC protein, prostate stromal 20 (ps20), encoded by the WFDC1 gene, is a potent growth inhibitory factor, and shares with other WFDC proteins the ability to modulate wound healing processes and immune responses to viral infections. However, ps20 remains relatively uncharacterised at the protein level. Read More

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September 2016

RNA structure through multidimensional chemical mapping.

Authors:
Siqi Tian Rhiju Das

Q Rev Biophys 2016 01;49:e7

Department of Biochemistry,Stanford University,Stanford,CA 94305,USA.

The discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire transcriptomes in vivo, but the resulting one-dimensional data generally remain too information-poor to allow accurate de novo structure determination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Read More

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January 2016

Developing ICP-MS/MS for the detection and determination of synthetic DNA-protein crosslink models via phosphorus and sulfur detection.

Anal Bioanal Chem 2015 Mar 5;407(9):2433-7. Epub 2015 Feb 5.

Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45220-0172, USA.

Various endogenous and exogenous agents drive the un-directed formation of covalent bonds between proteins and DNA. These complex molecules are of great biological relevance, as can derive in mutations, but are difficult to study because of their heterogeneous chemical properties. New analytical approaches with sufficient detection capabilities to detect and quantify these compounds can help to standardize study models based on synthesized standards. Read More

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Analysis of transmembrane domains and lipid modified peptides with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry.

Anal Chem 2014 Apr 24;86(8):3722-6. Epub 2014 Mar 24.

Heidelberg University Biochemistry Center , Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.

Protein-lipid interactions within the membrane are difficult to detect with mass spectrometry because of the hydrophobicity of tryptic cleavage peptides on the one hand and the noncovalent nature of the protein-lipid interaction on the other hand. Here we describe a proof-of-principle method capable of resolving hydrophobic and acylated (e.g. Read More

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A new nuclease member of the FAN club.

Nat Struct Mol Biol 2010 Aug;17(8):926-8

To cope with the life-threatening crisis of a DNA interstrand cross-link (ICL), human cells must invoke the Fanconi anemia (FA) DNA repair pathway. The FA pathway is a multistep repair process, requiring multiple nucleolytic incisions and translesion DNA synthesis. Recent work from four laboratories has identified a novel FA-associated nuclease, FAN1, that binds directly to monoubiquitinated FANCD2, resolving a decade-long puzzle regarding the function of this FANCD2 modification. Read More

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Tandem mass spectrometry for the determination of the sites of DNA interstrand cross-link.

J Am Soc Mass Spectrom 2004 Nov;15(11):1565-71

Department of Chemistry, University of California at Riverside, Riverside, California 92521-0403, USA.

Formation of DNA interstrand cross-link is implicated in the mechanism of anticancer activity of some drugs. Here we examined the fragmentation of deprotonated ions of double-stranded oligodeoxynucleotides (ODNs) that are covalently held together with either a mitomycin C or a 4,5',8-trimethylpsoralen. Our results showed that, upon collisional activation, the covalently-bound duplex ODNs cleaved to give a series of wn and [an-base] ions; the sites of interstrand cross-linking could be determined from the mass shifts of some product ions. Read More

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November 2004

Solubilization and partial characterization of extensin fragments from cell walls of cotton suspension cultures. Evidence for a covalent cross-link between extensin and pectin.

Plant Physiol 1995 Aug;108(4):1691-701

Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater 74078, USA.

Extensin, a major hydroxyproline (Hyp)-rich glycoprotein in walls of cultured cells of dicotyledonous plants, is very difficult to solubilize. To learn about the nature of the insolubilization, we have tested the ability of a variety of selective hydrolytic methods, and combinations of them, to liberate extensin or fragments of extensin from suspension-culture cell walls. After the complete deglycosylation of cotton (Gossypium hirsutum L. Read More

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