FULL PAPER
DOI: 10.1002/chem.200902169
Oxidation of an Oligonucleotide-Bound CeIII/Multiphosphonate Complex for
Site-Selective DNA ACHTNUTGRNEUNGScission
Tuomas Lçnnberg,[a, b] Yuichiro Aiba,[a] Yuya Hamano,[a] Yoshitaka Miyajima,[a]
Jun Sumaoka,[a] and Makoto Komiyama*[a]
Abstract:
conjugates
N,N,N’,N’-tetrakis(methylenephospho-
ACHTUNGTRENNUNGnic acid) (EDTP) have been used to
Oligodeoxyribonucleotide
of ethylenediamine-
linkage. No cleavage occurs at the
other single-stranded regions, which
suggests that the catalytic Ce species is
strictly localized next to the target
phosphodiester linkage. No decrease in
the reaction rate is observed upon in-
troduction of scavengers for hydroxyl
radicals (such as DMSO or MeOH) or
singlet oxygen (such as NaN3) to the
system; this indicates that the reaction
proceeds via a hydrolytic pathway. Any
significant contribution by an oxidative
pathway is further ruled out by the ob-
servation that nucleosides remain
intact after incubation with CeIV/EDTP
complex for extended periods.
place a CeIII/EDTP complex in close
proximity to predetermined phospho-
diester linkages of a complementary
target oligonucleotide. In the presence
of atmospheric oxygen, the CeIII is oxi-
dized into CeIV which, in turn, efficient-
ly cleaves the target phosphodiester
Keywords: cerium · DNA · DNA
cleavage · hydrolysis
Introduction
cleaving agents that are directly compatible with enzymatic
DNA manipulation used in current molecular biology and
biotechnology.
Preparation of man-made cutters for site-selective scission
of DNA has been one of the most attractive and challenging
themes of bioorganic chemistry, mainly because of their po-
tential applications in advanced molecular biology, therapy,
and many other fields.[1,2] Many elegant systems utilizing ox-
idative cleavage of the target DNA have already been de-
veloped and used for various purposes (e.g., structural
probes of DNA/protein or DNA/drug interactions, as well as
inhibition of target gene expression). Artificial hydrolytic
cutters, which cut DNA at a desired site through hydrolysis
of the target phosphodiester linkage, on the other hand,
have been limited in number despite great demand for
Among the metal catalysts reported to hydrolyze the im-
mensely stable phosphodiester linkages in DNA, CeIV ion is
characterized by its high scission activity, being able to hy-
drolyze DNA under physiological conditions.[3] In previous
papers,[4] a single-stranded DNA substrate was selectively
cleaved at the target site by addition of CeIV salts (e.g.,
CeACHTUNTRGENNUG(NH4)2ACHUTNGTREN(NGUN NO3)6) to oligonucleotide–ligand conjugates (or
peptide nucleic acid–ligand conjugates), thus placing the
CeIV complexes at a predetermined site (Figure 1b). In
these artificial cutters, however, large excess of the CeIV salt
to the conjugate (e.g., 100–1000 fold) is usually needed for
efficient cleavage due to competitive formation of the hy-
droxide gel of CeIV around pH 7.[5,6] The large excess of
CeIV, in turn, gives rise to off-target scission at other single-
stranded regions of the target DNA. Clearly, further im-
provements in site selectivity and scission efficiency are re-
quired for more versatile and practical applications of these
tools.
[a] Dr. T. Lçnnberg,+ Y. Aiba,+ Y. Hamano,+ Dr. Y. Miyajima,
Dr. J. Sumaoka, Prof. M. Komiyama
Research Center for Advanced Science and Technology
The University of Tokyo, 4-6-1 Komaba, Meguro-ku
Tokyo 153-8904 (Japan)
Fax : (+81)03-5452-5209
This paper describes a novel strategy for the preparation
of well-characterized CeIV-based site-selective cutters for
single-stranded DNA scission. As depicted in Figure 1a, an
easily tractable CeIII salt, which is markedly less prone to gel
formation, is used as a precursor of the catalytically active
CeIV species. As a ligand, ethylenediamine-N,N,N’,N’-tetra-
[b] Dr. T. Lçnnberg+
Current address: Department of Chemistry
The University of Turku, Vatselankatu 2, Turku 20014 (Finland)
[+] T.L. started this work, and Y.A. and Y.H. completed it.
Supporting information for this article is available on the WWW
Chem. Eur. J. 2010, 16, 855 – 859
ꢀ 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
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