A metallo base-pair incorporating a terpyridyl-like motif: Bipyridyl-pyrimidinone·Ag(I)·4-pyridine

Article abstract of DOI:10.1039/b709291a

The design and characterization of a geometrically unique, metallo base-pair motif is reported. The Royal Society of Chemistry.

Full text of DOI:10.1039/b709291a

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A metallo base-pair incorporating a terpyridyl-like motif: bipyridyl-
pyrimidinone?Ag(I)?4-pyridine{
Dongwon Shin and Christopher Switzer*
Received (in Cambridge, UK) 19th June 2007, Accepted 3rd August 2007
First published as an Advance Article on the web 20th August 2007
DOI: 10.1039/b709291a
The starting point for the design of the terpyridine-like motif
was our recently reported Ni(II) base-pairs incorporating symme-
trical bipyridine-like ligands.7h,i These Ni(II) pairs incorporate
pyridyl-pyrimidinone or -purine bases. Formal migration of the
pyridyl group from one side of a bis-bipyridine-like base-pair motif
results in the Pyrbipy?Mn+?Py pair displayed in Fig. 1. Due to its
asymmetry, the latter has the advantage of greater information
content over self-pairs. A density functional calculation{ was
performed initially using Ni(II) as the metal, but later with Ag(I), to
ascertain the geometric properties of Pyrbipy?Mn+?Py. The results
are shown in Fig. 1 (top right and bottom). The calculation
predicts that a motif incorporating a 4-pyridyl group more closely
The design and characterization of a geometrically unique,
metallo base-pair motif is reported.
DNA is an attractive target for molecular engineering as its
structural alternatives are relevant to therapeutics,1 materials
chemistry,2 synthetic biology3 and molecular evolution.4 Alteration
of base-pair structure has been a repeated object of study,5 and has
led to an expanded set of base-pairs, including those that interact
via hydrogen-bonds or hydrophobically.6 Metal ion coordination
has emerged as a third means of inducing DNA double strand
interactions.7 We report the design and characterization of the first
metallo base-pair incorporating
Pyrbipy?Ag+?4-Py (Fig. 1).
a
terpyridyl-like motif,
…
approximates the 9.05 A N1 N1 distance found in a natural
˚
DNA helix than a motif bearing a 3-pyridyl group, where the
˚
corresponding distances are 7.7 and 6.4 A, respectively.
Superposition of the calculated geometry for Pyrbipy?Ag+?Py on
an A?T DNA base-pair (bottom of Fig. 1) provided further
support for the choice of a 4-pyridyl over a 3-pyridyl group.
Independent of design considerations, both 4- and 3-pyridyl
substituted nucleosides were prepared as described below to allow
their properties in a helix to be compared. Syntheses of the pyridyl
deoxyriboside phosphoramidites are shown in Fig. 2. Several
syntheses are known for the 3- and 4-pyridyl deoxyribosides.8
However, we were attracted to methodology reported by Reese
and Wu9 for the synthesis of 4-amino-3-pyridyl deoxyribosides as
it provided a unified approach to the synthesis of our 3- and
4-pyridyl targets, and gave the prospect of improved efficiency.
Thus, 29-deoxyribonolactone 1 was transformed into 2 and 3 by a
reaction with the appropriate lithio-pyridine followed by reduction
of the resulting keto–lactol mixture with L-selectride. Cyclization
of 2 and 3 under Mitsunobu conditions gave 29-deoxyribofurano-
sides 4 and 5 with .98 and 87% diastereomeric excess,
respectively, in favor of the beta isomers. The remaining
transformations to arrive at phosphoramidites 10 and 11 were
uneventful.
Bipyridylpyrimidinone phosphoramidite 14 was obtained from
12 in five steps as shown in Fig. 3. Bipyridylpyrimidinone
nucleoside 13 was accessed through a Stille coupling between the
4-chloro-2-pyrimidinone derived from 12 and tributylstannyl
bipyridine.
The oligonucleotides listed in Table 1 bearing Pyrbipy, 4-Py, 3-Py
and natural nucleobases were prepared on a DNA synthesizer
using standard protocols. Purification was accomplished via
polyacrylamide gel electrophoresis. Oligonucleotide identity was
confirmed by MALDI-TOF mass spectrometry.
Fig. 1 Top left: 4-(20-Bipyridyl)pyrimidinone?Ag+?4-pyridine base-pair;
top right: B3LYP/SDD,6-31G* geometry of Pyrbipy?Ag+?Py comparing the
N–C distances of optimal 4-pyridyl and suboptimal 3-pyridyl geometries;
bottom: superposition of the Pyrbipy?Ag+?Py B3LYP/SDD,6-31G* struc-
ture on an A?T pair.
Department of Chemistry, University of California–Riverside, Riverside,
CA, 92521, USA. E-mail: switzer@ucr.edu; Fax: 951-827-2435;
Tel: 951-827-7266
{ Electronic supplementary information (ESI) available: Experimental
procedures and spectral information. See DOI: 10.1039/b709291a
Melting temperatures of the oligonucleotide duplexes are listed
in Table 1. Only Ag+ was found to significantly stabilize the duplex
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Chem. Commun., 2007, 4401–4403 | 4401

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Table 1 DNA duplex melting temperatures in the presence and
absence of metal ions in addition to Na+. Samples contained 2.5 mM of
each DNA strand, 5 mM non-sodium metal ion where indicated,
50 mM NaNO3, and 10 mM HEPES, pH 7
59-d-CTTTCTYTCCCT
39-d-GAAAGAXAGGGA
X/Y
M
Tm/uC
X/Y
M
Tm/uC
Pyrbipy/4-Py
—
22.3
35.2
25.3
25.2
23.4
23.1
22.1
21.8
21.4
21.1
22.0
26.5
Pyrbipy/T
Pyrbipy/C
Pyrbipy/A
Pyrbipy/G
A/T
—
23.4
25.9
25.1
28.6
22.3
27.3
22.6
28.0
34.1
38.7
38.0
41.0
31.9
30.8
Ag+
Co2+
Zn2+
Cu2+
Ni2+
Mn2+
Mg2+
Tl+
Ag+
—
Ag+
—
Ag+
—
Ag+
—
Fe2+
—
Ag+ a
—
Pyrbipy/3-Py
G/C
Ag+
Ag+ a
—
Pyrbipy/ Pyrbipy
Ag+
a
Silver(I) ion was added in these cases as a control.
stability in comparison to the matched Pyrbipy?Ag+?4-Py pair
(Table 1). Control experiments with natural duplexes (X/Y = G/C
or A/T) in the presence of Ag+ showed stability enhancements
consistent with the well-known interaction of this metal ion with
DNA helices.10
Fig. 2 Synthesis of 29-deoxyribofuranosyl 3- and 4-pyridyl nucleoside
phosphoramidites. Reagents and conditions: (a) 3- or 4-pyridyl bromide,
n-butyllithium, diethyl ether, 278 uC; (b) L-Selectride, THF, 278 uC; (c)
DIAD, Ph3P, THF, 0 uC; (d) Et3N?(HF)3, THF, 0 uC; (e) DMTCl,
pyridine, RT; (f) bis(diisopropyl)aminocyanoethoxychlorophosphine,
Et(Pri)2N, CH2Cl2, 0–25 uC.
One possible explanation of the metal ion binding preference of
Pyrbipy/4-Py considers two factors: (i) the stacking/unstacking of
the terpyridyl-like group upon release/binding of a metal ion, and
(ii) the enthalpy associated with metal ion dehydration. In
connection to the first point, the geometry of the metal pair in
the bottom of Fig. 1 suggests that metal ion binding places the
bipyridyl moiety of Pyrbipy outside of the base stack in B-DNA,§
and, inter alia, that metal ion release might permit the pyridyl
groups sufficient freedom to move within the base stack, possibly
forming a zipper motif.11 On balance, Ag+ appears to overcome
both considerations better in that its ability to p-coordinate12 may
recover some of the stacking energy lost upon metal ion binding,
and its enthalpy of hydration is lower in comparison to divalent
ions.13
bearing a Pyrbipy/4-Py site, yielding a Tm of 35.2 uC. This result
equates to a 12.9 uC stabilization relative to the duplex in the
absence of Ag+ (Tm = 22.3 uC). Notable is the lack of appreciable
stabilization of the Pyrbipy/4-Py containing duplex by Ni2+, the
metal ion found to have a strong affinity for the bis-bipyridyl-like
structure (e.g., Pyrpy/Pyrpy).7h,i
To ascertain the importance of the geometrical features of the
Pyrbipy?Ag+?4-Py pair for stability, the alternative Pyrbipy?Ag+?3-Py
pair was examined (lower left of Table 1). Here the stabilization in
the presence vs. the absence of Ag+ was reduced to 4.5 uC. Thus,
the Pyrbipy?Ag+?4-Py pair has enhanced stabilization in comparison
to Pyrbipy?Ag+?3-Py, in keeping with modeling studies (vide supra).
Exploration of mispairs of Pyrbipy with both natural nucleobases
and itself in the presence and absence of Ag+ showed diminished
In conclusion, Pyrbipy pairs selectively with 4-Py over 3-Py and
natural nucleobases in the presence of Ag+. This result
demonstrates the viability of a terpyridyl-like base-pair in DNA,
Fig. 3 Synthesis of 29-deoxyribosyl-1-(4-(20,60,2--bipyridyl))pyrimidinone phosphoramidite. Reagents and conditions: (a) SOCl2, DMF, CHCl3, reflux; (b)
2-tributylstannyl-6-pyridylpyridine, Pd(Ph3P)4, toluene, reflux; (c) ammonia, methanol; (d) DMTCl, pyridine, RT; (e) bis(diisopropyl)aminocyanoethoxy
chlorophosphine, Et(Pri)2N, CH2Cl2, 0–25 uC.
4402 | Chem. Commun., 2007, 4401–4403
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and suggests Pyrbipy?Ag+?4-Py may be orthogonal to metallo-pairs
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This work was supported by DOD/DARPA/DMEA under
award no. DMEA90-02-2-0216 and the University of California–
Riverside.
Notes and references
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PA, 2003.
§ A circular dichroism spectrum of the Pyrbipy?Ag+?4-Py bearing duplex is
included in the ESI.{
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