title: Effect of different N7 substitution of dinucleotide cap analogs on the hydrolytic susceptibility towards scavenger decapping enzymes (DcpS).
abstract: Scavenger decapping enzymes (DcpS) are involved in eukaryotic mRNA degradation process. They catalyze the cleavage of residual cap structure m(7)GpppN and/or short capped oligonucleotides resulting from exosom-mediated the 3' to 5' digestion. For the specific cap recognition and efficient degradation by DcpS, the positive charge at N7 position of guanine moiety is required. Here we examine the role the N7 substitution within the cap structure on the interactions with DcpS (human, Caenorhabditis elegans and Ascaris suum) comparing the hydrolysis rates of dinucleotide cap analogs (m(7)GpppG, et(7)GpppG, but(7)GpppG, bn(7)GpppG) and the binding affinities of hydrolysis products (m(7)GMP, et(7)GMP, but(7)GMP, bn(7)GMP). Our results show the conformational flexibility of the region within DcpS cap-binding pocket involved in the interaction with N7 substituted guanine, which enables accommodation of substrates with differently sized N7 substituents.
authors.affiliation: Faculty of Chemistry, University of Warsaw, 1 Pasteura St., 02-093 Warsaw, Poland.
authors.forename: Karolina
authors.initials: K
authors.lastname: Piecyk
authors.affiliation: Centre of New Technologies, University of Warsaw, 2c Banacha St., 02-097 Warsaw, Poland; Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 93 Zwirki & Wigury St., 02-089 Warsaw, Poland.
authors.forename: Zbigniew M
authors.initials: ZM
authors.lastname: Darzynkiewicz
authors.affiliation: Faculty of Chemistry, University of Warsaw, 1 Pasteura St., 02-093 Warsaw, Poland; Department of Biochemistry, Second Faculty of Medicine, Medical University of Warsaw, 101 Zwirki & Wigury St., 02-089 Warsaw, Poland.
authors.forename: Marzena
authors.initials: M
authors.lastname: Jankowska-Anyszka
authors.affiliation: Centre of New Technologies, University of Warsaw, 2c Banacha St., 02-097 Warsaw, Poland; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 93 Zwirki & Wigury St., 02-089 Warsaw, Poland.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Ferenc-Mrozek
authors.affiliation: Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 93 Zwirki & Wigury St., 02-089 Warsaw, Poland.
authors.forename: Janusz
authors.initials: J
authors.lastname: Stepinski
authors.affiliation: Centre of New Technologies, University of Warsaw, 2c Banacha St., 02-097 Warsaw, Poland; Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 93 Zwirki & Wigury St., 02-089 Warsaw, Poland.
authors.forename: Edward
authors.initials: E
authors.lastname: Darzynkiewicz
authors.affiliation: Centre of New Technologies, University of Warsaw, 2c Banacha St., 02-097 Warsaw, Poland. Electronic address: e.bojarska@cent.uw.edu.pl.
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Bojarska
mesh_terms: D000818:Animals; D017165:Ascaris suum / Q000235:genetics / Q000378:metabolism; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004722:Endoribonucleases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D057075:Enzyme Assays; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006801:Humans; D007527:Isoenzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D009690:Nucleic Acid Conformation; D011755:Pyrophosphatases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012314:RNA Cap Analogs / Q000737:chemistry* / Q000378:metabolism; D020871:RNA Stability / Q000235:genetics*; D011993:Recombinant Fusion Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D055672:Static Electricity
chemical_list: D029742:Caenorhabditis elegans Proteins; D007527:Isoenzymes; D012314:RNA Cap Analogs; D011993:Recombinant Fusion Proteins; D004722:Endoribonucleases; C485332:DcpS protein, human; D011755:Pyrophosphatases; C509343:dcs-1 protein, C elegans
keywords: Cap analogs; Decapping scavengers; Enzyme kinetic; Fluorescence titration; mRNA degradation