Synthesis of a novel nucleoside for alternative DNA base pairing through metal complexation

Full text of DOI:10.1021/jo990326u

5002
J . Org. Chem. 1999, 64, 5002-5003
Ch a r t 1
Syn th esis of a Novel Nu cleosid e for
Alter n a tive DNA Ba se P a ir in g th r ou gh Meta l
Com p lexa tion
Kentaro Tanaka and Mitsuhiko Shionoya*
Institute for Molecular Science, Okazaki National Research
Institutes, Myodaiji, Okazaki 444-8585, J apan
Received February 22, 1999
Chemical modification of nucleic acid constituents has
gained more and more attention from the viewpoints of
medicinal chemistry as well as material sciences. So far, a
large number of nonnatural analogues of DNA nucleosides
have been synthesized,1 and in particular, it has been
generally accepted that the incorporation of metal complexes
into oligonucleotides is a key design target for the function-
alization of DNA.2 In recent years, a variety of oligonucleo-
tides containing photoactive and redox-active metal com-
plexes have been constructed for the development of energy
and electron-transfer systems through DNA, DNA hybrid-
ization probes and sensors, and site-specific DNA cleavage.
In the DNA duplex formation, hydrogen bonding is one
of the most principal driving forces as well as the main factor
of sequence specificity in the hybridization. An alternative
approach we have used for the incorporation of metal
complexes into oligonucleotides is the more direct changing
of a DNA base itself into a chelator-containing nucleobase.
In this strategy, hydrogen-bonded base pairing is replaced
by metal-assisted base pairing, thereby creating a novel
binding motif in duplex DNA.3 Such an approach would
provide a wide range of applications based on its use as the
third base pair along with the other two natural base pairs,
AT and GC, and on the metal alignment through DNA
duplex formation. The molecule we have chosen to synthe-
size and study is a â-C-nucleoside4 having a phenylenedi-
amine as the chelator-type base, 9, which was expected to
form a 2:1 square-planar complex with a metal ion such as
Pd2+, Pt2+, Cu2+, and Ni2+ (Chart 1). In addition, the metal-
assisted base pair would have geometrical analogy to a
natural base pair.
A scheme for the synthesis of the phenylenediamine â-C-
nucleoside 9 is shown in Scheme 1. We first tried the
coupling reaction of organocadmium species of the pro-
tected phenylenediamine derivatives with the well-known
R-chlorosugar of Hoffer (2-deoxy-3,5-di-O-p-toluoyl-R-D-
erythro-pentofuranosyl chloride).5 However, the preparation
of organomagnesium species before transmetalation was not
successful. Then as starting material for the synthesis of 9
the readily available ribonolactone, 2,3,5-tri-O-benzyl-D-
ribonic γ-lactone,6 and the STABASE (N-1,1,4,4-tetrameth-
yldisililazacyclopentane) adduct of 4-bromo-o-phenylenedi-
amine7 1 were used. The coupling and the conversion to
deoxyribonucleoside followed the synthesis of C-nucleosides
by Leumann et al.8 It is well-known that this coupling
reaction is not applicable to the 2′-deoxy analogue of ribono-
lactone due to enolization at C(2) under the conditions.8b
Lithiation-substitution methodology was applicable to the
stabase adduct of 1. Treatment of this adduct with nBuLi
at -78 °C and in situ reaction with ribonolactone and the
subsequent benzoyl protecting of amino groups furnished a
mixture of hemiacetal 2 in 36% yield in two steps. The
reduction of 2 with excess of Et3SiH/BF3‚Et2O provided only
the naturally configured â-epimer 3. The anomeric config-
uration of 3 was determined in a close connection with the
structural assignment for 8 as mentioned afterward. De-
benzylation of 3 with BBr3 provided the N-protected ribo-
C-nucleoside 4 in 85% yield. Selective protection of the 3′-
and 5′-hydroxyl groups with TIPDSCl2 in pyridine gave 5
in 82% yield. Treatment of 5 with p-tolyl chlorothionoformate
followed by homolytic reductive cleavage of the C-O bond
with AIBN and nBu3SnH afforded 2′-deoxy derivative 7
quantitatively. Desilylation of 7 with tetra-n-butylammo-
nium fluoride provided the N-protected phenylenediamine
2′-deoxy-C-nucleoside 8, which was then converted into the
free C-nucleoside 9 by treatment with aqueous NaOH.9
* To whom correspondence should be addressed. Present address:
Department of Chemistry, School of Science, University of Tokyo,
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, J apan. e-mail: shionoya@
chem.s.u-tokyo.ac.jp.
(1) (a) Lesser, D. R.; Kurpiewski, M. R.; J en-J acobson, L. Science 1990,
250, 776. (b) Kornberg, A.; Baker, T. A. DNA Replication, 2nd ed.; W. H.
Freeman: New York, 1992. (c) SantaLucia, J .; Kierzek, R.; Turner, D. H.
Science 1992, 256, 217. (d) Smith, S. A.; Rajur, S. B.; McLaughlin, L. W.
Nature Struct. Biol. 1994, 1, 198. (e) Schweuzer, B. A.; Kool, E. T. J . Am.
Chem. Soc. 1995, 117, 1863. (f) Ren, R. X.-F.; Chaudhuri, N. C.; Paris, P.
L.; Rumney IV, S.; Kool, E. T. J . Am. Chem. Soc. 1996, 118, 7671.
(2) Selected examples: (a) Dreyer, G. R.; Dervan, P. B. Proc. Natl. Acad.
Sci. U.S.A. 1985, 82, 968. (b) Chen, C.-H. B.; Sigman, D. S. J . Am. Chem.
Soc. 1988, 110, 6570. (c) Telser, J .; Cruickshank, K. A.; Schanze, K. S.;
Netzel, T. L. J . Am. Chem. Soc. 1989, 111, 7221. (d) Bannwarth, W.;
Pfleiderer, W.; Mu¨ller, F. Helv. Chim. Acta 1991, 74, 1991 and references
therein. (e) Murphy, C. J .; Arkin, M. R.; J enkins, Y.; Ghatlia, N. D.;
Bossmann, S. H.; Turro, N. J .; Barton, J . K. Science 1993, 262, 1029. (f)
Bashkin, J . K.; Frolova, E. I.; Sampath, U. J . Am. Chem. Soc. 1994, 116,
5981. (g) Matsumura, K.; Endo, M.; Komiyama, M. J . Chem. Soc., Chem.
Commun. 1994, 2019. (h) Magda, D.; Miller, R. A.; Sessler, J . L.; Iverson,
B. L. J . Am. Chem. Soc. 1994, 116, 7439. (i) Meade, T. J .; Kayyem, J . F.
Angew. Chem., Int. Ed. Engl. 1995, 34, 352. (j) Hall, J .; Hu¨sken, D.; Ha¨ner,
R. Nucleic Acids Res. 1996, 24, 3522. (k) Manchanda, R.; Dunham, S. U.;
Lippard, S. J . J . Am. Chem. Soc. 1996, 118, 5144. (l) Schliepe, J .; Berghoff,
U.; Lippert, B.; Cech, D. Angew. Chem., Int. Ed. Engl. 1996, 35, 646. (m)
Mucic, R. C.; Herrlien, M. K.; Mirkin, C. A.; Letsinger, R. L. Chem. Commun.
1996, 555. (n) Dandliker, P. J .; Holmlin, R. E.; Barton, J . K. Science 1997,
275, 1465. (o) Meggers, E.; Kusch, D.; Giese, B. Helv. Chim. Acta 1997, 80,
640. (p) Ihara, T.; Nakayama, M.; Murata, M.; Nakano, K.; Maeda, M. Chem.
Commun. 1997, 1609. (q) Magda, D.; Crofts, S.; Lin, A.; Miles, D.; Wright,
M.; Sessler, J . L. J . Am. Chem. Soc. 1997, 119, 2293. (r) Hurley, D. J .; Tor,
Y. J . Am. Chem. Soc. 1998, 120, 2194 and references therein.
1
The anomeric configuration for 8 was determined by H
NOE experiments and by examination of coupling constants
(4) For reviews of C-glycoside synthesis, see: (a) The Chemistry of
C-Glycosides; Levy, D. E., Tang, C., Ed.; Pergamon: Oxford, 1995. (b)
C-Glycoside Synthesis; Postema, M. H. D., Ed.; CRC Press: Boca Raton,
1995.
(5) Hoffer, M. Chem. Ber. 1960, 93, 2777.
(6) Timpe, W.; Dax, K.; Wolf, N.; Weidmann, H. Carbohydr. Res. 1975,
35, 53.
(7) Sato, N.; Kuriyama, H.; Agoh, M. Eur. Pat. 252507 A1, J an 13, 1988.
(8) (a) Hildbrand, S.; Leumann, C. Angew. Chem., Int. Ed. Engl. 1996,
35, 1968. (b) Hildbrand, S.; Blaser, A.; Parel, S. P.; Leumann, C. J . Am.
Chem. Soc. 1997, 119, 5499.
(9) Millican, T. A.; Mock, G. A.; Chauncey, M. A.; Patel, T. P.; Eaton, M.
A. W.; Gunning, J .; Cutbush, S. D.; Neidle, S.; Mann, J . Nucleic Acids Res.
1984, 12, 7435.
(3) It is noteworthy in this connection that Marzilli et al. have recently
reported the effect of T-Hg-T cross-links, where T represents a thymine
base, on DNA conformational changes such as hairpin-duplex transition.
See: Kuklenyik, Z.; Marzilli, L. G. Inorg. Chem. 1996, 36, 5654.
10.1021/jo990326u CCC: $18.00 © 1999 American Chemical Society
Published on Web 06/17/1999

Communications
J . Org. Chem., Vol. 64, No. 14, 1999 5003
Sch em e 1a
a
Reagents and conditions: (a) 1,2-bis(chlorodimethylsilyl)ethane, DBU, DMF, 120 °C, 82%; (b) (i) nBuLi, 2,3,5-tri-O-benzyl-D-ribonic γ-lactone,
THF, -78 °C, 0 °C; (ii) benzoyl chloride, triethylamine, CH2Cl2, 0 °C, rt, 36% (two steps); (c) triethylsilane, BF3‚OEt2, CH2Cl2, -78 °C, rt, 88%; (d)
BBr3, CH2Cl2, -78 °C, rt, 85%; (e) TIPDSCl2, pyridine, 0 °C, rt, 82%; (f) O-p-tolyl chlorothionoformate, DMAP, MeCN, rt, 97%; (g) AIBN, nBu3SnH,
toluene, 80 °C, 99%; (h) nBu4NF, THF, rt, 83%; (i) NaOH, H2O, 80 °C, 14%.
F igu r e 2. ESI mass spectrum of Pd2+ complex 10: 553.2 ([ML2
- H+]+ calcd 553.13), 330.0 ([ML]+ calcd 330.02), 276.8 ([ML2]2+
calcd 277.07), 224.0 ([L]+ calcd 224.12), where M ) Pd2+, L )
nucleoside 9.
resonances in the aromatic region as well as those in the
ribose moiety shifted to lower field almost in proportion to
increasing concentration of Pd2+, and when the concentra-
tion of Pd2+ reached half the concentration for 9 the
complexation was completed. This result shows that 9 and
Pd2+ form a stable 2:1 complex 10 with a high binding
constant. Although there are two possible structures (cis and
trans) for complex 10, we observed only one species in the
NMR spectra. The electrospray ionization (ESI) mass spec-
trum also provided clear evidence for the 2:1 complexation
(Figure 2).
The present work demonstrates a convenient synthesis
F igu r e 1. 500 MHz 1H NMR spectra of nucleoside 9 with
of a â-C-nucleoside-containing phenylenediamine as a “che-
lator-base” moiety, providing an alternative DNA base
pairing through metal complexation. The site-specific incor-
poration of the newly synthesized nucleoside into oligo-
nucleotides is now underway.
increasing amounts of Pd2+. [1] ) 26 mM in D2O. [Pd2+]/[9] ) (a)
0.00, (b) 0.08, (c) 0.19, (d) 0.38, (e) 0.49, (f) 0.57.
for 1′- and 2′-protons as done by Kool et al.1f In â-anomers,
the 2′R-proton is only near the 1′-proton. When the 1′-proton
was irradiated, we observed a 4% enhancement at the 2′R-
proton. The epimer 8 had a 1′-resonance which appeared as
a nearly evenly spaced doublet of doublets (J ) 6.4 and 10.7
Hz). This 1′-2′ coupling constant trend is consistent with
similar coupling constants reported for related â-C-
nucleosides.1f,10
Ack n ow led gm en t. This work is supported by Grant-
in-Aids for Scientific Research on Priority Areas (No.
10149101 “Metal-assisted Complexes”, No. 08249103 “Bio-
metalics”, and No. 706 “Dynamic Control of Stereochem-
istry”) from the Ministry of Education, Science, Sports and
Culture, J apan.
Complex formation between nucleoside 9 and Pd2+ in D2O
was followed by 1H NMR spectroscopy (Figure 1). Proton
Su p p or tin g In for m a tion Ava ila ble: Synthetic procedures
and analytical data for selected new compounds. This material is
available free of charge via the Internet at http://pubs.acs.org.
(10) The product should be carefully handled due to its instability in
solution under aerobic conditions. Indeed, nucleoside 9 was used directly
for the subsequent metal complexation study after rapid purification.
J O990326U