scholarly journals 5-Carboxylcytosine is resistant towards phosphodiesterase I digestion: implications for epigenetic modification quantification by mass spectrometry

RSC Advances ◽  
2019 ◽  
Vol 9 (50) ◽  
pp. 29010-29014 ◽  
Author(s):  
Fang Yuan ◽  
Ying Bi ◽  
Jia-Yuan Zhang ◽  
Ying-Lin Zhou ◽  
Xin-Xiang Zhang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Snake Venom ◽  
Epigenetic Modification ◽  
Dna Hydrolysis ◽  
Snake Venom Phosphodiesterase

5-Carboxylcytosine is found to be resistant to snake venom phosphodiesterase I (PDE1), a 3′ to 5′ exonuclease commonly used in several DNA hydrolysis protocols.

scholarly journals Capillary Monolithic Bioreactor of Immobilized Snake Venom Phosphodiesterase for Mass Spectrometry Based Oligodeoxynucleotide Sequencing

2011 ◽  
Vol 84 (2) ◽  
pp. 1157-1164 ◽  
Author(s):  
Chao Zhao ◽  
Ruichuan Yin ◽  
Junfa Yin ◽  
Dapeng Zhang ◽  
Hailin Wang
Keyword(s):  
Mass Spectrometry ◽  
Snake Venom ◽  
Snake Venom Phosphodiesterase

scholarly journals Stereochemistry of hydrolysis by snake venom phosphodiesterase.

1979 ◽  
Vol 254 (16) ◽  
pp. 7476-7478 ◽  
Author(s):  
P.M. Burgers ◽  
F. Eckstein ◽  
D.H. Hunneman
Keyword(s):  
Snake Venom ◽  
Snake Venom Phosphodiesterase

Synthesis of phosphoramidate analogs of ribodinucleoside phosphates

1979 ◽  
Vol 44 (3) ◽  
pp. 792-798 ◽  
Author(s):  
Alexei V. Azhayev ◽  
Alexander A. Krayevsky ◽  
Jiří Smrt
Keyword(s):  
Snake Venom ◽  
Pancreatic Ribonuclease ◽  
Carbon Tetrabromide ◽  
Snake Venom Phosphodiesterase

Cytidine 5'-phosphate (Ia) reacts with 1,1'-carbonyldiimidazole under the formation of 2',3'-O-carbonylcytidine 5'-phosphorimidazolidate (IIa) which affords (by the action of 3'-amino-3'-deoxyadenosine (IIIa)) 3'-deoxyadenosine-3'-amidophosphoryl-(3' → 5')-cytidine (IVa) and (by the action of 3'-amino-3-deoxy-N6-dimethyladenosine (IIIc)) 3'-deoxy-N6-dimethyladenosine-3'-amidophosphoryl-(3' → 5')-cytidine (IVc). Starting from adenosine 5'-phosphate (Ib) and 3'-amino-3'-deoxycytidine (IIIb) or the substance IIIc, 3'-deoxycytidine-3'-amidophosphoryl-(3' → 5')-adenosine (IVb) or 3'-deoxy-N6-dimethyladenosine-3'-amidophosphoryl-(3' → 5')-adenosine (IVd) were prepared. 6-Azauridine (V) was transformed, by the action of triphenylphosphine, lithium azide and carbon tetrabromide, followed by the action of triphenylphosphine and ammonia, to 5'-amino-5'-deoxy-6-azauridine (VI). The substance VI was transformed by the action of 2',3'-O-carbonyl-adenosine 5'-phosphorimidazolidate (IIb), to adenylyl-(5' → 5')-5'-amino-5'-deoxy-6-azauridine (VII). The compound IVb is not degraded by snake venom and spleen phosphodiesterases and is degraded by pancreatic ribonuclease to adenosine and the compound IIIb. The compound VII is degraded by snake venom phosphodiesterase to adenosine and the compound VI.

Analysis of O2′-Methylnucleoside 5′-Phosphates in Snake Venom Hydrolysates of RNA: Identification of O2′-Methyl-5-Carboxymethyluridine as a Constituent of Yeast Transfer RNA

1975 ◽  
Vol 53 (7) ◽  
pp. 735-746 ◽  
Author(s):  
M. W. Gray
Keyword(s):  
Snake Venom ◽  
Deae Cellulose ◽  
Anion Exchange Chromatography ◽  
Exchange Chromatography ◽  
Assay Method ◽  
Blocking Group ◽  
Wheat Embryo ◽  
Yeast Trna ◽  
Snake Venom Phosphodiesterase ◽  
Hydrolysis Of

Snake venom phosphodiesterase liberates the O2′-methylnucleoside (Nm) constituents of RNA as the corresponding 5′-nucleotides (pNm), which, in contrast to normal 5′-nucleotides (pN), are resistant to dephosphorylation by venom 5′-nucleotidase. This property provides the basis of a convenient and highly reproducible quantitative assay for Nm residues in RNA. The assay method involves: (1) hydrolysis of RNA with whole or partially-purified snake venom; (2) isolation of the pNm derivatives, as a group, by anion-exchange chromatography on DEAE-cellulose; (3) resolution of the individual pNm compounds by two-dimensional paper chromatography; (4) identification and quantitative measurement of pNm derivatives by ultraviolet absorption spectrophotometry. Using this procedure, the molar proportions of the Nm constituents of wheat embryo, yeast, and Escherichia coli tRNA have been determined. The close correspondence between the values measured by venom hydrolysis and those obtained by analysis of alkali-stable dinucleotide (Nm-Np) sequences attests to the validity of the venom assay, and further indicates that alkali-stable sequences larger than dinucleotides are not present in significant amounts in the tRNA of the above three organisms.During the present investigation, several ultraviolet-absorbing components, not immediately identifiable as ribose-methylated nucleotides, were isolated along with the expected O2′-methylnucleoside 5′-phosphates. Preliminary characterization of one of these compounds suggests that it is a derivative of a novel nucleoside, O2′-methyl-5-carboxymethyluridine (cm5Um). Venom hydrolysis of yeast tRNA liberates the 5′-nucleotide of cm5Um in the form of a carboxyl-blocked derivative (pU-2). During alkaline hydrolysis of yeast tRNA, the blocking group in U-2 is labilized and cm5Um is released as part of an alkali-stable dinucleotide, cm5Um-Ap. The proportion of pU-2 in venom hydrolysates of yeast tRNA (0.02 mol%, the same as the content of cm5Um-Ap in alkaline hydrolysates) suggests that O2′-methyl-5-carboxymethyluridine may be confined to a single isoaccepting species of tRNA in yeast.In an allied study, reinvestigation of the alkali-stable dinucleotide sequences of baker's yeast tRNA has confirmed previous results concerning the sequence distribution of O2′-methylribose in yeast tRNA (Gray, M. W. &Lane, B. G. (1967) Biochim. Biophys. Acta 134, 243–257).

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