The pK(a) of the internucleotidic 2'-hydroxyl group in diribonucleoside (3'-->5') monophosphates.
Ionization of the internucleotidic 2'-hydroxyl group in RNA facilitates transesterification reactions in Group I and II introns (splicing), hammerhead and hairpin ribozymes, self-cleavage in lariat-RNA, and leadzymes and tRNA processing by RNase P RNA, as well as in some RNA cleavage reactions promoted by ribonucleases. Earlier, the pK(a) of 2'-OH in mono- and diribonucleoside (3'-->5') monophosphates had been measured under various nonuniform conditions, which make their comparison difficult. This work overcomes this limitation by measuring the pK(a) values for internucleotidic 2'-OH of eight different diribonucleoside (3'-->5') monophosphates under a set of uniform noninvasive conditions by 1H NMR. Thus the pK(a) is 12.31 (+/-0.02) for ApG and 12.41 (+/-0.04) for ApA, 12.73 (+/-0.04) for GpG and 12.71 (+/-0.08) for GpA, 12.77 (+/-0.03) for CpG and 12.88 (+/-0.02) for CpA, and 12.76 (+/-0.03) for UpG and 12.70 (+/-0.03) for UpA. By comparing the pK(a)s of the respective 2'-OH of monomeric nucleoside 3'-ethyl phosphates with that of internucleotidic 2'-OH in corresponding diribonucleoside (3'-->5') monophosphates, it has been confirmed that the aglycons have no significant effect on the pK(a) values of their 2'-OH under our measurement condition, except for the internucleotidic 2'-OH of 9-adeninyl nucleotide at the 5'-end (ApA and ApG), which is more acidic by 0.3-0.4 pK(a) units.
Acharya
S
S
Department of Bioorganic Chemistry, Box 581, Biomedical Center, Uppsala University, S-751 23 Uppsala, Sweden.
Földesi
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A
Chattopadhyaya
J
J
D004722:Endoribonucleases / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D017665:Hydroxyl Radical / Q000737:chemistry* / Q000493:pharmacokinetics*; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular; D012313:RNA / Q000737:chemistry*; D012326:RNA Splicing; D016337:RNA, Catalytic / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D043262:Ribonuclease P; D012265:Ribonucleotides / Q000737:chemistry* / Q000493:pharmacokinetics*; D013329:Structure-Activity Relationship
D016337:RNA, Catalytic; D012265:Ribonucleotides; C418481:hairpin ribozyme; C427204:hammerhead ribozyme; D017665:Hydroxyl Radical; D012313:RNA; D012343:RNA, Transfer; D004722:Endoribonucleases; D043262:Ribonuclease P