Templated synthesis of highly stable, electroactive, and dynamic metal-DNA branched junctions

Article abstract of DOI:10.1002/anie.200703741

(Figure Presented) Templated metalation of DNA junctions allows incorporation of a range of transition metals into DNA assemblies. The resulting highly stable metal-DNA junctions can be assembled into dynamic multinuclear structures, with metal centers as their corners and DNA single strands as their sides. Ready and reversible structural switching of these assemblies with external agents (see picture) allows for control of geometry and metal-metal distances.

Full text of DOI:10.1002/anie.200703741

Angewandte
Chemie
DOI: 10.1002/anie.200703741
DNA Nanotechnology
Templated Synthesis of Highly Stable, Electroactive, and Dynamic
Metal–DNA Branched Junctions**
Hua Yang and Hanadi F. Sleiman*
DNA has recently emerged as a promising template to create
nanostructures with precisely programmed features.[1] Typical
approaches involve the assembly of branched units containing
unmodified oligonucleotides.[1,2] In contrast, the incorpora-
tion of transition metals into the vertices of DNA nano-
structures is much less explored.[3] This is despite the
tremendous potential of metals to influence both the function
of DNA nanostructures, through their redox, photophysical,
magnetic, and catalytic properties, as well as the structure of
DNA nanoassemblies, through the plethora of geometries
and coordination numbers available to them.[3–9] The devel-
opment of metal–DNA nanostructures is currently hampered
by the need to use metals that are kinetically inert, resist the
harsh conditions of oligonucleotide solid-phase synthesis, and
do not preferentially bind or react with the DNA bases or
phosphate backbone.[3] Furthermore, the limited examples of
metal–DNA nanostructures have contained metal centers
separated by DNA double strands, which reduces metal-metal
interactions.[3] In order to harness the potential of transition
metals as functional corner units in DNA assembly, a more
systematic approach that bypasses these limitations is neces-
sary.
Herein, we present a template approach that allows for
the incorporation of normally labile metal centers, such as
copper(I), copper(II), and silver(I), into DNA branch points
(Scheme 1a). Remarkably high structural stability and chir-
ality transfer to the metal complex are demonstrated. More-
over, we have used this approach to generate the first example
of a dynamic multimetallic metal–DNA assembly, with three
metal complexes as the corners, single-stranded DNA as the
sides, and multiple DNA double strands at the periphery
(Scheme 1d). We demonstrate quantitative and reversible
structural switching of these metal–DNA nanostructures by
adding specific DNA strands, resulting in controlled modu-
lation of the metal–metal distances. This contribution thus
allows the programmable generation of structurally dynamic
multimetallic metal–DNA assemblies, with anticipated appli-
cations in nanoelectronics, nanooptics, artificial photosyn-
thesis, high-density data storage, and catalysis.
To create stable and electroactive metal–DNA junctions,
we examined the attachment of the ligand bis(2,9-diphenyl)-
1,10-phenanthroline (dpp) to DNA (Scheme 1a). This ligand
has been used by the groups of Sauvage and others to
generate interwoven structures.[10] It forms complexes such as
[Cu(dpp)2]+, whose redox potential falls within the compat-
ible window for DNA bases (+ 0.8 to À0.7 V vs. saturated
calomel electrode, SCE),[11] and evidence of partial interca-
lation of these complexes into DNA has been provided.[12] An
ethylene glycol substituted, monotritylated phosphoramidite
derivative of dpp was thus synthesized (Scheme 1b, dpp
vertex).[13,15] The resulting molecule can be incorporated at
any position of a DNA strand using standard solid-phase
DNA synthesis, allowing for in-strand complexation of metal
centers.
To introduce labile metal centers into DNA vertices, we
examined the use of DNA strands as templates to bring two
dpp units into close proximity (Scheme 1a). To realize this
approach, two complementary 10-mer DNA strands (1 and 1’)
terminated with dpp at their 5’ and 3’ ends were synthesized.
Hybridization of 1 and 1’ and subsequent addition of
1.1 equivalents of either Cu+, Cu2+, or Ag+ resulted in
quantitative formation of the metal(dpp)2–DNA junctions
2·CuI, 2·CuII, and 2·AgI (Scheme 1a, Figure 1a). Denaturation
of the DNA arms of these junctions resulted in a single
electrophoresis band of significantly lower mobility than 1
and 1’, showing that the new compounds are held together by
metal coordination (Figure 1a). In contrast, untemplated
complexation, by incubation of 1 or 1’ separately with these
metals, was not possible.[14,15] The structures of 2·CuI, 2·CuII,
and 2·AgI were confirmed by MALDI-TOF mass spectrom-
etry and spectroscopic experiments.[15] Notably, complexation
of the normally five-coordinate CuII center is shown by its
green color and UV/vis bands typical of [Cu(phen)2]2+, while
the pink-red CuI–DNA complex has a spectrum typical of
[Cu(phen)2]+ and shows fluorescence at 405 nm upon excita-
tion at 330 nm in aqueous solution.[15]
Interestingly, the resulting metal–DNA junctions show
dramatically enhanced stability (Figure 1b). While the melt-
ing temperature (Tm) of ligand-appended dpp–DNA helix 2 is
slightly higher (528C) than an unmodified duplex (438C),
silver coordination increases the Tm to 648C, and the Tm of
2·CuI is as high as 808C (Figure 1b).[16] This increase is one of
the highest reported in melting temperature (+ 378C for a 10-
mer) for an appended metal–DNA complex[17] and suggests
significant stabilization of the DNA base stack through
interaction with the metal unit.
[*] H. Yang, Prof. H. F. Sleiman
Department of Chemistry, McGill University
801 Sherbrooke Street West
Montreal Quebec H3A 2K6 (Canada)
Fax: (+1)514-398-3797
E-mail: hanadi.sleiman@mcgill.ca
[**] NSERC, CFI, CSACS, CIFAR. H.F.S. is a Cottrell Scholar of the
Research Corporation
Circular dichroism (CD) spectroscopy of the metal(dpp)2–
DNA junctions suggests chirality transfer from DNA to the
metal unit (Figure 1c,d). Without metal coordination, the CD
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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Scheme 1. a) dpp–DNA 1 and 1’ hybridize to form 2; 2 reacts with AgI, CuII, or CuI to form complexes 2·AgI, 2·CuII, or 2·CuI; 2·CuI is oxidized to
2·CuII by I2/H2O; 2·CuII is reduced to 2·CuI by tris(2-carboxyethyl)phosphine. b) 2,9-Diphenyl-1,10-phenanthroline phosphoramidite (dpp vertex)
used for in-strand DNA labeling. OMMTr=4-monomethoxytrityl. c) AMBER local minimum energy structure of 2·CuI. d) Formation and dynamic
switching of 7CuI3 and 8·CuI3.
right-handed helical twist of metal–bis(dpp) complexes,
resulting in CD features that are similar to those obtained
from 2·AgI and 2·CuI.[21] This finding is consistent with likely
chirality transfer from the DNA duplex to the dpp2–CuI unit,
which induces a helical arrangement of the dpp ligands.
Preliminary AMBER force-field calculations show a right-
handed helical arrangement of the two dpp ligands in these
metal–DNA junctions (i.e., following the right-handed B-
DNA helix).[15] It is of note that this CD peak, which
dominates the spectrum of the metal–DNA junction, arises
from a single metal center which is only a minor part of the
entire structure (one metal center per 10-mer DNA duplex).
The CD spectrum of the CuII–DNA junction 2·CuII reveals
two dominant positive bands, consistent with UV/vis bands of
[Cu(phen)2]2+ (Figure 1d).[19,20] Interestingly, the copper–
DNA junction can be cleanly and reversibly cycled between
the + 1 and + 2 oxidation states. Addition of the reducing
Figure 1. a) Denaturing polyacrylamide gel electrophoresis (PAGE).
agent tris(2-carboxyethyl)phosphine (TCEP) completely
Lane 1: 1, lane 2: 1’, lane 3: 2, lane 4: 2·AgI, lane 5: 2·CuII, lane 6:
reverts the CD spectrum of 2·CuII into a spectrum identical
to 2·CuI. In turn, addition of I2/H2O to 2·CuI restores the CuII
CD bands.[15] This is one of the rare examples of transition
metal–DNA systems that can cycle between two redox states
(only ferrocene–DNA and ruthenium-bipyridine-acetylacet-
onate–DNA systems were previously reported).[22] The strong
CD signatures associated with the metals in these junctions
can be used as diagnostic peaks for both the nature of the
metal and its specific oxidation state.
Transition metal–DNA structures have been used as
probes of energy and charge transport,[4] sequence-specific
nucleases,[5] and detection systems.[6] DNA has been meta-
lated by reduction of metal ions around its backbone[7] and by
2·CuI. b) Melting temperature curves. Unmodified DNA 3: Tm =438C,
2: Tm =528C, 2·AgI: Tm =648C, 2CuI: Tm =808C. c) CD spectra of 2
and 3. d) CD spectra of 2·AgI, 2·CuI, and 2·CuII.
spectrum of double-stranded dpp–DNA 2 is similar to an
unmodified B-DNA duplex 3 (Figure 1c).[18] However, after
metal coordination, the CD spectrum changes significantly.
Complexes 2·AgI and 2·CuI, both with d10 metals, show
significant reduction in the positive B-DNA band and the
appearance of a large positive peak at 342 nm, which
dominates the spectrum. This peak coincides with a UV/vis
transition typical of these metal complexes.[19,20] Previous
reports have shown that attached chiral sugars can induce a
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creation of “bases” that can serve as ligands.[8] DNA has also
templated the assembly of organic modules through metal–
salen complexes.[9] A few recent studies have attached inert
transition metals to the ends of DNA duplexes to create 1D
and 2D assemblies.[3] In contrast to these approaches, the
DNA-templated method described herein creates a unique
coordination environment, which is able to induce the
normally labile d10 metals CuI (which is very unstable in
water), AgI, and CuII to form highly stable metal–DNA
junctions.
In addition to mononuclear metal–DNA units, this
approach can readily generate multinuclear structures con-
taining precisely positioned metals and DNA strands
(Scheme 1d). Three building blocks (4, 5, and 6) were
synthesized by solid-phase DNA protocols as before. Each
of these contains three DNA regions separated by two dpp
ligands. Two outer 10-mer DNA sequences work as template
regions to mediate the assembly of a DNA triangle and to
direct the metalation of the (dpp)2 units (Scheme 1d). The
three internal 15-mer sequences serve as single-stranded sides
in the triangle and allow structural switching of this molecule
with external agents (see below).
Self-assembly of the desired metalated triangle is highly
efficient. Sequential hybridization of 4, 5, 6 shows quantita-
tive formation of the dimer 4:5 and triangle 7 on native PAGE
(Figure 2a, lanes 1–3). Addition of 3.3 equivalents CuI to
metalate all three sites shows near quantitative product
formation to give 7·CuI3 (Figures 2a and 3a). The CD
spectrum of 7·CuI3 is similar to the mononuclear DNA
junction 2·CuI (Figure 2b). Denaturation of the DNA arms
results in a single band of significantly lower mobility than 4,
5, and 6, showing that 7·CuI3 is held together by metal
coordination (Figure 3a, lane 5). To ascertain that 7·CuI3 is a
fully tris-metallated closed triangle, we synthesized a mono-
metallated dimer (4:5·CuI2, Figure 3b, lane 1) and an open,
bis-metallated trimer that does not have the proper sequence
to cyclize (9·CuI2, Figure 3b, lane 3) and showed the mobility
of 7·CuI3 (Figure 3a, lane 2) to be distinct from either of these
structures. It is of note that, unlike in previous studies,[1–3] the
assembly of this cyclic structure is quantitative, and no
oligomeric byproducts are formed. We believe this to be due
to the presence of single-stranded, flexible sides in triangle 7,
which can relieve any strain that may arise from the
cyclization of its three components.
Figure 2. a) 16% Native PAGE. a) Lane 1: 4, lane 2: 4:5, lane 3: 7,
lane 4: 7·CuI3, lane 5: 8·CuI3, lane 6: addition of s1 to 8·CuI3, forms
7·CuI3 +s1, lane 7: s1:s2. b) CD spectra of 7 and 7·CuI3.
Unlike previous methods in DNA nanotechnology, which
typically yielded fully double-stranded constructs, the single-
stranded sides of triangle 7·CuI3 allow its ready functionaliza-
tion,[15] and impart it with dynamic character. Controlled
structural switching is demonstrated by using specific DNA
strands to reversibly compress and release this triangle, thus
tuning the distance between two of the metal centers
(Scheme 1d). Molecule s1 possesses two regions that are
complementary to two of the triangle sides (4 and 5) and
separated by a short organic spacer (C6). Addition of s1 to
7·CuI3 can compress this structure and bring two metal corners
close together, forming 8·CuI3 (Scheme 1d). In turn, addition
of s2, which is fully complementary to s1, can remove s1 and
release the original triangle (Scheme 1d). Both events can be
confirmed by native PAGE (Figure 2a, lanes 5 and 6).[15] Thus,
Figure 3. a) 14% Denaturing PAGE. Lane 1: 4, lane 2: 5, lane 3: 6,
lane 4: 7, lane 5: 7·CuI3. b) 14% Denaturing PAGE. Lane 1: 4:5·CuI2,
lane 2: 7·CuI3, lane 3: 9·CuI2.
copper–DNA triangle 7·CuI3 can undergo controlled and
reversible structural switching with added DNA strands,
resulting in modification of its geometry and modulation of
the distance between its electroactive metal centers.
In summary, we have shown a new, DNA-templated
method to create metal–DNA branch points which are
electroactive and highly stable, thus allowing the introduction
of normally kinetically labile transition metals into DNA
junctions. Furthermore, this approach gives access to multi-
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Communications
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Received: August 14, 2007
Revised: November 16, 2007
Keywords: DNA · nanostructures · redox chemistry ·
.
self-assembly · transition metals
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[15] Please see the Supporting Information for more details.
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