a
Th e p K of th e In ter n u cleotid ic 2′-Hyd r oxyl Gr ou p in
Dir ibon u cleosid e (3′f5′) Mon op h osp h a tes
S. Acharya, A. F o¨ ldesi, and J . Chattopadhyaya*
Department of Bioorganic Chemistry, Box 581, Biomedical Center,
Uppsala University, S-751 23 Uppsala, Sweden
Received October 9, 2002
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
monophosphates had been measured under various nonuniform conditions, which make their
comparison difficult. This work overcomes this limitation by measuring the pK values for
internucleotidic 2′-OH of eight different diribonucleoside (3′f5′) monophosphates under a set of
a
of 2′-OH in mono- and diribonucleoside (3′f5′)
a
1
uniform noninvasive conditions by H NMR. Thus the pK
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 s of the
a
is 12.31 ((0.02) for ApG and 12.41 ((0.04)
a
respective 2′-OH of monomeric nucleoside 3′-ethyl phosphates with that of internucleotidic 2′-OH
in corresponding diribonucleoside (3′f5′) 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
In tr od u ction
a
units.
5
7
talysis and in ribonuclease action, as well as in tRNA
2
c
1-7
processing by RNase P RNA. The biological importance
of the 2′-OH group makes determination of its pK
extremely important issue in terms of understanding the
structure and function of RNA in molecular details. It
is, however, not possible to measure the pK of 2′-OH of
a
a larger RNA than a dimer in an unambiguous and
1
The 2′-OH group distinguishes RNA from DNA both
a
an
2
,3
3,4
functionally as well as structurally. It is involved in
3
,4
recognition,
processing, and catalytic properties of
5
RNA, such as the stereospecific transesterification reac-
tions involved in the Group I and Group II splicing
reactions,3 self-cleavage in lariat-RNA, and RNA ca-
h,i
6
accurate manner, since it decomposes readily under
alkaline conditions.8 Several attempts
9-22
have been
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0.1021/jo026545o CCC: $25.00 © 2003 American Chemical Society
Published on Web 02/04/2003
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J . Org. Chem. 2003, 68, 1906-1910