Phosphine containing oligonucleotides for the development of metallodeoxyribozymes

Article abstract of DOI:10.1039/b617871e

Novel transition metal catalysts based on oligonucleotides can be easily obtained by functionalization of 5-iodouridine with phosphine ligands, resulting in good asymmetric induction in palladium catalyzed allylic nucleophilic substitution. The Royal Society of Chemistry.

Full text of DOI:10.1039/b617871e

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Phosphine containing oligonucleotides for the development of
metallodeoxyribozymes{
Lo¨ıc Ropartz,a Nico J. Meeuwenoord,c Gijsbert A. van der Marel,c Piet W. N. M. van Leeuwen,b
Alexandra M. Z. Slawina and Paul C. J. Kamer*a
Received (in Cambridge, UK) 7th December 2006, Accepted 10th January 2007
First published as an Advance Article on the web 5th February 2007
DOI: 10.1039/b617871e
Obviously, the phosphine ligand needs to be introduced after
DNA synthesis to avoid exposure to the oxidation step. Liu et al.
developed a method for introduction of phosphine at the 39 and 59
ends.13 We decided to use (+)-5-iodo-29-deoxyuridine (IdU) as an
intermediate to enable phosphine introduction at any desired
position. DNA is the biomolecule of choice because it can be
synthesized more easily than RNA and it has much better
hydrolytic stability.
Novel transition metal catalysts based on oligonucleotides can
be easily obtained by functionalization of 5-iodouridine with
phosphine ligands, resulting in good asymmetric induction in
palladium catalyzed allylic nucleophilic substitution.
Catalysis plays a key role in chemical conversions by making them
faster and more selective. The rates and selectivities of enzymatic
catalysis are seldom equalled by man-made transition metal
catalysts, which are responsible for the majority of production in
the chemical industry. More and more attempts are being made to
use the concepts of biology in order to obtain efficient catalysts
that can compete with enzymes, such as incorporation of transition
metal complexes in proteins1 and antibodies.2 The interest in DNA
double-helix structures has nowadays shifted from its initial area of
biological research to reach all domains of science.3 Nucleic acids
are at least as powerful in molecular recognition as peptides,4,5
while their application in transition metal catalysis has hardly been
explored.6,7 Indeed, the application of oligonucleotides as cata-
lysts8 or as scaffolds for transition metal catalysts6,9 is an emerging
field of research. A great advantage of oligonucleotides over
proteins is that the secondary structure can be easily engineered,
resulting in the design of countless possibilities of 3-dimensional
structures10 and conformations of DNA.11
Palladium catalyzed coupling of diphenylphosphine to the
commercially available IdU leads to the desired functionalized
nucleoside compound (dppdU, Fig. 1) in high yield (.95%)
(Scheme 1). A catalytic amount (1–3%) of Pd(OAc)2 and a slight
excess of diphenylphosphine are used to obtain fast and complete
conversion of IdU. The 5-iodo-39,59-di-O-acetyl-29-deoxyuridine
(AcIdU) is also easily converted to the corresponding AcdppdU.
This compound is surprisingly more prone to oxidation than its
counterpart dppdU and must be purified under anaerobic
conditions.14
Although the reaction proceeds smoothly for the 5-iodo-
29-deoxyuridine, higher palladium loadings (up to stoichiometric
amount) are required for the conversion of the supported
oligonucleotides dAIdUdT and dCIdUdG into the corresponding
dAdppdUdT and dCdppdUdG. Adsorption of the metal on the
CPG support (controlled pore glass), poor mass transport and Pd
coordination to the base pairs are believed to be responsible for the
poor efficiency of the catalytic coupling. Indeed, faster conversion
is obtained for polystyrene supported oligonucleotides although a
substantial amount of palladium catalyst is still indispensable.
Our approach for the development of highly functionalized late
transition metal catalysts that are capable of selective molecular
recognition is the introduction of suitable phosphine ligands into
oligonucleotides. This enables the development of transition metal
deoxyribozymes with well-defined secondary structures based on
Watson–Crick base pairing. These DNA based metal complexes
can provide a new class of highly selective catalyst for demanding
transformations. The strong molecular recognition power of
oligonucleotides, combined with the catalytic properties of
transition metal phosphine complexes, enables catalytic reactions
for which no enzymes or ribozymes12 are known. The high
substrate specificity and affinity of aptamers5 could allow
conversion of a single substrate present, even at extremely low
concentrations, in complex mixtures, like those in biological
systems.
aSchool of Chemistry, University of St. Andrews, St. Andrews, Fife, UK
KY16 9ST. E-mail: pcjk@st-andrews.ac.uk; Fax: +44 (0)1334463808;
Tel: +44 (0)1334467285
bVan ’t Hoff Institute for Molecular Sciences, University of Amsterdam,
Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
cLeiden Institute of Chemistry, Gorlaeus Laboratories, University of
Leiden, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
{ Electronic supplementary information (ESI) available: Experimental
data of the compounds. See DOI: 10.1039/b617871e
Fig. 1 Crystal structure of dppdU.
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The major challenges in the development of hybrid catalysts
based on oligonucleotides and transition metal complexes are in
the field of important reactions like (asymmetric) catalytic carbon–
carbon and carbon–heteroatom bond forming reactions. Since the
most powerful catalysts for these reactions, rhodium and
palladium phosphine complexes, have not been used in nucleic
acid based systems, we have tested the (oligo)nucleotide based
phosphine ligand systems in palladium catalyzed allylic substitu-
tion as a model reaction. Good enantiomeric excess is obtained (up
to 82% for the S enantiomer) in asymmetric palladium catalyzed
allylic amination with the monodentate ligand dppdU (Scheme 2,
Tables 1 and 2). Such chiral induction is startling as the chiral
centers on the molecule are situated far away from the
coordinating phosphine and thus from the catalytic metal center
(see Fig. 1).
Scheme 1 Synthesis of 5-diphenylphosphine-29-deoxyuridine. R1 = R2 =
H (dppdU); R1 = R2 = Ac (AcdppdU); R1 = deoxyadenosine-3-
phosphate,
R2
=
deoxythymidine-5-phosphate
(trinucleotide
dAdppdUdT).
The diphenylphosphine-containing trimers are deprotected and
released from the solid support by treatment with a NH4OH–
methylamine aqueous solution for 2 h at 80 uC under an argon
atmosphere. Subsequently, traces of palladium are removed by
washing with acetonitrile and 1,2-bis(diphenylphosphino)ethane
(dppe) in CH2Cl2 to prevent oxidation of the phosphine catalyzed
by the metal in water. Finally the phosphine-modified oligonucleo-
tides are purified by FPLC under aerobic conditions to provide the
products in moderate yields (.40%).
Another remarkable result is the solvent effect on the reaction as
it reverses the stereoselectivity of the product. Whilst the reaction
in tetrahydrofuran (THF) gives 80% of the S enantiomer, we
obtain 16% ee of the R form in acetonitrile–THF (Table 1). The
enantioselectivity using AcdppdU is also dependent on the reaction
conditions as the opposite enantiomers are obtained when
switching from THF (S form) to dichloromethane (DCM)
(R form). The stereoselectivity is, however, highly reduced
(respectively 8% and 23%). The 59-hydroxy moiety seems,
therefore, to play an important role in the stereoselectivity of the
catalytic species. Hydrogen bonding interactions, as observed in
the solid-state structure, are probably influencing the structure in
solution also. Importantly, good conversions are also obtained
with the trinucleotides dAdppdUdT and dCdppdUdG in the
allylic amination reactions, albeit at the expense of the enantio-
selectivity. This is a good model reaction for the use of large DNA
sequences as ligands, showing that the approach of molecular
recognition by DNA aptamers5 can be used for this palladium
catalyzed reaction and also demonstrating that the reaction still
proceeds in an aqueous environment. Other nucleophiles like
N-methylbenzylamine and dimethyl malonate result in good
conversions with dppdU as the ligand in the allylic substitution
reaction (see Table 2).
The structure of dppdU (Fig. 1) confirms the successful
synthesis.{ The determined structure is chiral and shows complete
conservation of the stereointegrity of the nucleoside. The P–C
bond lengths are normal and the C–P–C bond angles are, as
expected, approximately tetrahedral. In the crystal, O(2) is
hydrogen bonded to both OH groups to give a layer structure;
the NH group also H-bonds to O(25). There are channels
containing the included [partial weight] water, which forms short
contacts to both of the OH groups.
The NMR studies of dppdU with palladium and platinum
complexes confirm the importance of the interaction between the
nucleoside and the solvent. Platinum complexes were studied to
distinguish between cis and trans coordination modes. Reaction of
platinum(II) Cl2Pt(CH3CN)2 with dppdU in THF–CDCl3 leads to
Scheme 2 Asymmetric allylic amination: addition of benzylamine to 1,3-
diphenyl-2-propenyl acetate.
Table 1 Palladium catalyzed allylic substitution of 1,3-diphenyl-2-propenyl acetate with benzylamine
Ligand (L)
Solvent
L : Pd ratio
Incubation time/h
Conversion (%)
ee (%)
Absolute configuration
dppdUa
THF
THF
THF
THF
CH3CN–THF
DMF
THF
DCM
DCM
0.5
2
2
4
2
2
2
2
2
0.5–4
.99
.99
.99
.99
.99
.99
.99
.99
.99
83
62
72
80
79
16
14
8
21
23
8–12
—
5
S
S
S
S
R
R
S
dppdUa
2
4–16
4
4
4
2
2
2
dppdUa
dppdUa
dppdUa
dppdUa
AcdppdUa
AcdppdUa
AcdppdUa
dAdppdUdTb
dAdppdUdTb
dCdppdUdGb
a
R
R
R
—
R
b
THF–H2O 3 : 1
H2O
THF–H2O 3 : 1
4
4
4
8–24
24
24
15
30
Reaction conditions: 7.5 mmol [Pd(allyl)Cl]2, benzylamine : propenyl acetate : Pd = 120 : 40 : 1, solvent 2 cm3, 25 uC, 24 h. Reaction
conditions: 0.5 mmol [Pd(allyl)Cl]2, benzylamine : propenyl acetate : Pd : K2CO3 = 120 : 40 : 1 : 120, solvent 1 cm3, 25 uC, 36 h.
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This research was financed by the NRSCC and the European
Union Marie Curie Excellence Grants, artizyme catalysis, contract
number (MEXT-2004-014320), http://europa.eu.int/mariecurie-
actions
Table 2 Asymmetric allylic substitution using dppdU as ligand
Conversion ee Absolute
Nucleophile Allyl
Solvent (%)
(%) configuration
THF
THF
.99a
82
70
S
S
Notes and references
{ Crystallographic data for dppdU: empirical formula C21H21N2O5P?
(H2O)0.25, formula weight = 416.87, temperature = 93(2) K, wavelength =
.99a
˚
0.71073 A, monoclinic, space group C2, a = 18.165(4) A, b = 5.1771(9) A,
˚
˚
3
21
˚
˚
c = 22.063(5) A, b = 108.12(3)u, V = 1972.0(7) A , Z = 4, m = 0.177 mm
,
Dc = 1.404 Mg m23, crystal size 0.2 6 0.1 6 0.01 mm, reflections collected
6287, independent reflections 3282 [Rint = 0.03]. Refinement method full-
matrix least-squares on F2, data/restraints/parameters 3282/4/278, good-
ness-of-fit on F2 = 1.110, R1 [I . 2s(I)] = 0.0527, wR2 = 0.1352, absolute
structure parameter = 0.02(14). CheckCIF does not reveal any serious
issues. CCDC 626863. For crystallographic data in CIF or other electronic
format see DOI: 10.1039/b617871e
THF
THF
.99b
.99b
15
12
S
S
a
1 (a) E. T. Kaiser and D. S. Lawrence, Science, 1984, 226, 505; (b)
M. E. Wilson and G. M. Whitesides, J. Am. Chem. Soc., 1978, 100, 306;
(c) D. Qi, C. M. Tann, D. Haring and M. D. Distefano, Chem. Rev.,
2001, 101, 3081; (d) M. T. Reetz, Proc. Natl. Acad. Sci. U. S. A., 2004,
101, 5716; (e) C. Letondor, N. Humbert and T. R. Ward, Proc. Natl.
Acad. Sci. U. S. A., 2005, 102, 4683; (f) L. Panella, J. Broos, J. Jin,
M. W. Fraaije, D. B. Janssen, M. Jeronimus-Stratingh, B. L. Feringa,
A. J. Minnaard and J. G. de Vries, Chem. Commun., 2005, 5656.
2 H. Yamaguchi, T. Hirano, H. Kiminami, D. Taura and A. Harada,
Org. Biomol. Chem., 2006, 4, 3571.
3 H.-A. Wagenknecht, Angew. Chem., Int. Ed., 2003, 42, 3204.
4 (a) C. Tuerk and L. Gold, Science, 1990, 249, 505; (b) A. D. Ellington
and J. W. Szostak, Nature, 1990, 346, 818; (c) T. Hermann and
D. J. Patel, Science, 2000, 287, 820.
5 S. D. Jayasena, Clin. Chem. (Washington, DC, U. S.), 1999, 45,
1628.
6 J. Brunner, A. Mokhir and R. Kraemer, J. Am. Chem. Soc., 2003, 125,
12410.
7 G. Roelfes and B. L. Feringa, Angew. Chem., Int. Ed., 2005, 44,
3230.
8 S. K. Silverman, Org. Biomol. Chem., 2004, 2, 2701.
9 G. Roelfes, A. J. Boersma and B. L. Feringa, Chem. Commun., 2006,
635.
Reaction conditions: 7.5 mmol [Pd(allyl)Cl]2, amine : allyl acetate :
Pd : L = 120 : 40 : 1 : 2, solvent 2 cm3, 25 uC, 24 h. Reaction
conditions: 7.5 mmol [Pd(allyl)Cl]2, nucleophile : BSA (N,O-bis-
(trimethylsilyl)acetamide) : allyl acetate : Pd : L = 120 : 120 : 40 : 1 :
2, KOAc 1 mg, solvent 2 cm3, 25 uC, 2 h.
b
the formation of Cl2Pt(dppdU)2 in a cis conformation, showing a
singlet in the 31P NMR spectrum at d = 15.7 ppm with large
platinum–phosphine coupling (satellite JP–Pt = 5344 Hz). When the
same complex is formed in acetonitrile-d3–methanol (2 drops
added for solubility), the 31P NMR spectrum shows a signal at d =
14.2 ppm with a considerably smaller platinum–phosphine
coupling (satellite JP–Pt = 2660 Hz), indicating a change to a trans
conformation. Also, a single complex is obtained when dppdU is
reacted with MeClPd(COD), showing a singlet in the 31P NMR
spectrum (d = 22.3 ppm, DMSO-d6) characteristic of a trans
complex.
In summary, we report the Pd catalyzed synthesis of nucleosides
and oligonucleotides functionalized with phosphine moieties and
their use as ligands for asymmetric catalytic substitution reactions.
Secondary interactions (such as hydrogen bonding) are believed to
rule the transfer of chirality from the distant sugar to the
phosphine as both the solvent and the substituent of the ribose
modify the stereoselectivity of the reaction. Importantly, the
catalytic reaction does proceed in water as solvent, which allows
the use of longer DNA sequences. This opens an efficient route to
introduce a phosphine ligand at any position of oligonucleotides,
adding an important new possibility for the application of DNA
aptamers in the field of transition metal catalysis.
10 P. W. K. Rothemund, Nature, 2006, 440, 297.
11 E. Winfree, F. Liu, L. A. Wenzler and N. C. Seeman, Nature, 1998, 394,
539; N. Seeman, Biochemistry, 2003, 42, 7259; B. Samori and
G. Zuccheri, Angew. Chem., Int. Ed., 2005, 44, 1166.
12 T. R. Cech, Science, 1987, 236, 1532.
13 (a) K. Sakurai, T. M. Snyder and D. R. Liu, J. Am. Chem. Soc., 2005,
127, 1660; (b) Z. J. Gartner, M. W. Kanan and D. R. Liu, J. Am. Chem.
Soc., 2002, 124, 10304.
14 The alternative routes, protection of the dppdU phosphoramidite
compound by BH3 during DNA synthesis or deprotection of the
oligonucleotides from the support followed by a palladium catalyzed
P–C coupling reaction in an aqueous medium, failed to give the expected
product.
1558 | Chem. Commun., 2007, 1556–1558
This journal is ß The Royal Society of Chemistry 2007