Branchpoint Sugar Stereochemistry Determines the Hydrolytic Susceptibility of Branched RNA Fragments by the Yeast Debranching Enzyme (YDBR)

ChemInform ◽  
2004 ◽  
Vol 35 (9) ◽  
Author(s):  
Sandra Carriero ◽  
Maria M. Mangos ◽  
Kazim A. Agha ◽  
Anne M. Noronha ◽  
Masad J. Damha
Keyword(s):  
Debranching Enzyme ◽  
Rna Fragments ◽  
Branched Rna ◽  
Sugar Stereochemistry

Branchpoint Sugar Stereochemistry Determines the Hydrolytic Susceptibility of Branched RNA Fragments by the Yeast Debranching Enzyme (YDBR)

2003 ◽  
Vol 22 (5-8) ◽  
pp. 1599-1602 ◽  
Author(s):  
Sandra Carriero ◽  
Maria M. Mangos ◽  
Kazim A. Agha ◽  
Anne M. Noronha ◽  
Masad J. Damha
Keyword(s):  
Debranching Enzyme ◽  
Rna Fragments ◽  
Branched Rna ◽  
Sugar Stereochemistry

scholarly journals A homolog of lariat-debranching enzyme modulates turnover of branched RNA

RNA ◽  
2014 ◽  
Vol 20 (8) ◽  
pp. 1337-1348 ◽  
Author(s):  
Stephen M. Garrey ◽  
Adam Katolik ◽  
Mantas Prekeris ◽  
Xueni Li ◽  
Kerri York ◽  
...  
Keyword(s):  
Debranching Enzyme ◽  
Branched Rna

scholarly journals Design, Synthesis, and Properties of Phosphoramidate 2′,5′-Linked Branched RNA: Toward the Rational Design of Inhibitors of the RNA Lariat Debranching Enzyme

2015 ◽  
Vol 80 (20) ◽  
pp. 10108-10118 ◽  
Author(s):  
Nobuhiro Tago ◽  
Adam Katolik ◽  
Nathaniel E. Clark ◽  
Eric J. Montemayor ◽  
Kohji Seio ◽  
...  
Keyword(s):  
Rational Design ◽  
Design Synthesis ◽  
Debranching Enzyme ◽  
Branched Rna

Conformational properties of branched RNA fragments in aqueous solution

Biochemistry ◽  
1988 ◽  
Vol 27 (17) ◽  
pp. 6403-6416 ◽  
Author(s):  
Masad J. Damha ◽  
Kelvin K. Ogilvie
Keyword(s):  
Aqueous Solution ◽  
Conformational Properties ◽  
Rna Fragments ◽  
Branched Rna

scholarly journals Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1

2016 ◽  
Vol 113 (51) ◽  
pp. 14727-14732 ◽  
Author(s):  
Nathaniel E. Clark ◽  
Adam Katolik ◽  
Kenneth M. Roberts ◽  
Alexander B. Taylor ◽  
Stephen P. Holloway ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Nucleophilic Attack ◽  
X Rays ◽  
Turnover Rates ◽  
Optimal Position ◽  
Debranching Enzyme ◽  
Aerobic Conditions ◽  
Bona Fide ◽  
Branched Rna ◽  
Retroviral Infections

Intron lariats are circular, branched RNAs (bRNAs) produced during pre-mRNA splicing. Their unusual chemical and topological properties arise from branch-point nucleotides harboring vicinal 2′,5′- and 3′,5′-phosphodiester linkages. The 2′,5′-bonds must be hydrolyzed by the RNA debranching enzyme Dbr1 before spliced introns can be degraded or processed into small nucleolar RNA and microRNA derived from intronic RNA. Here, we measure the activity of Dbr1 fromEntamoeba histolyticaby using a synthetic, dark-quenched bRNA substrate that fluoresces upon hydrolysis. Purified enzyme contains nearly stoichiometric equivalents of Fe and Zn per polypeptide and demonstrates turnover rates of ∼3 s−1. Similar rates are observed when apo-Dbr1 is reconstituted with Fe(II)+Zn(II) under aerobic conditions. Under anaerobic conditions, a rate of ∼4.0 s−1is observed when apoenzyme is reconstituted with Fe(II). In contrast, apo-Dbr1 reconstituted with Mn(II) or Fe(II) under aerobic conditions is inactive. Diffraction data from crystals of purified enzyme using X-rays tuned to the Fe absorption edge show Fe partitions primarily to the β-pocket and Zn to the α-pocket. Structures of the catalytic mutant H91A in complex with 7-mer and 16-mer synthetic bRNAs reveal bona fide RNA branchpoints in the Dbr1 active site. A bridging hydroxide is in optimal position for nucleophilic attack of the scissile phosphate. The results clarify uncertainties regarding structure/function relationships in Dbr1 enzymes, and the fluorogenic probe permits high-throughput screening for inhibitors that may hold promise as treatments for retroviral infections and neurodegenerative disease.

Biophysical Measurement of Molecular Weight of Foot-and-Mouth Disease RNA Fragments

1974 ◽  
Vol 32 ◽  
pp. 262-263
Author(s):  
Sydney S. Breese ◽  
Howard L. Bachrach
Keyword(s):  
Chemical Properties ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Distilled Water ◽  
Bovine Plasma ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Carbon Coated ◽  
Rna Fragments ◽  
Physical And Chemical

Continuing studies on the physical and chemical properties of foot-and-mouth disease virus (FMDV) have included electron microscopy of RNA strands released when highly purified virus (1) was dialyzed against demlneralized distilled water. The RNA strands were dried on formvar-carbon coated electron microscope screens pretreated with 0.1% bovine plasma albumin in distilled water. At this low salt concentration the RNA strands were extended and were stained with 1% phosphotungstic acid. Random dispersions of strands were recorded on electron micrographs, enlarged to 30,000 or 40,000 X and the lengths measured with a map-measuring wheel. Figure 1 is a typical micrograph and Fig. 2 shows the distributions of strand lengths for the three major types of FMDV (A119 of 6/9/72; C3-Rezende of 1/5/73; and O1-Brugge of 8/24/73.

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