Synthesis of DNA triangles with vertexes of Bis(terpyridine)iron(II) complexes

Article abstract of DOI:10.1021/ja048537q

The synthesis of the terpyridine derivative 1 tethered to a DNA oligonucleotide and its use for the preparation of two-way branched metal-organic modules capable of self-assembling into DNA triangles are described. Copyright

Full text of DOI:10.1021/ja048537q

Published on Web 06/26/2004
Synthesis of DNA Triangles with Vertexes of Bis(terpyridine)iron(II)
Complexes
Jin Seok Choi,† Chang Won Kang,† Kisung Jung,† Jung Woon Yang,† Yang-Gyun Kim,‡ and
Hogyu Han*,†
Department of Chemistry, Korea UniVersity, Seoul 136-701, Korea, and Department of Biochemistry,
College of Medicine, Chung-Ang UniVersity, Seoul 156-756, Korea
Received March 13, 2004; E-mail: hogyuhan@korea.ac.kr
Scheme 1. Use of Terpyridine-DNA Conjugates for the
Preparation of Two-Way Branched Metal-Organic Modules
Capable of Self-Assembling into DNA Trianglesa
Molecular self-assembly offers a powerful means of fabricating
well-defined and complex structures from simple components in a
programmable manner.1 Recently, DNA molecules have been used
to create DNA-based nanostructures and to direct the assembly of
other functional molecules.2,3 DNA nanotechnology takes advantage
of the ability of DNA to form the double helix and unusual structural
motifs through Watson-Crick base pairing. In particular, immobile
analogues of the Holliday junction serve as a stable, branched
junction with four double helical arms. However, the limited number
of available DNA motifs applicable to the self-assembly of DNA
restricts the possible construction of geometric DNA objects in more
diverse and sophisticated arrangements. The development of novel
versatile junctions would therefore greatly assist the further
extension of the DNA role in a material world.
Here, we report the synthesis of the terpyridine derivative whose
dimeric metal complex can be used as an alternative to the Holliday
junction (Scheme 1). This terpyridine derivative allowed the
preparation of terpyridine-DNA conjugates that formed two-way
branched metal-organic modules upon dimerization of terpyridine
ligands in the presence of Fe(II) ions. These modules self-assembled
into DNA triangles in which each vertex and side consist of a bis-
(terpyridine)Fe(II) complex and a DNA duplex, respectively.
The terpyridine derivative 1 was synthesized as shown in Scheme
2.4 Oxidation of compound 24a-d with molecular oxygen in the
presence of potassium tert-butoxide afforded 3.4e Subsequent
esterification of 3 with thionyl chloride in refluxing methanol
followed by complete reduction using NaBH4 provided 5. A
coupling reaction between 5 and (3-bromopropoxy)-tert-butyldim-
ethylsilane using NaH afforded 6, which was then oxidized to
methyl sulfone 7 with 3-chloroperoxybenzoic acid. After converting
the TBDMS to the DMT group, the methylsulfonyl group of 9 was
displaced by cyanide ion to give 10. Basic hydrolysis and
iodomethane treatment4f of 10 afforded 11, which was subsequently
reduced to the final product 1 by use of NaBH4. A CPG-coupled
terpyridine derivative 12 was prepared by succinylation of the 4′-
hydroxyl group of 1 followed by coupling to LCAA-CPG beads
with HOBt/BOP coupling reagents.5 Subsequent capping of unre-
acted free amines on the CPG with acetic anhydride was performed
to prevent nonspecific coupling of bases to the support during
oligonucleotide synthesis. Spectrophotometric analysis (A504) of
DMT cations released upon treatment of 12 with trichloroacetic
acid/CH2Cl2 (5:95) confirmed 28 µmol/g loading of 1 onto the CPG
support.
a Modules contain a bis(terpyridine)Fe(II) complex X tethered by its
4-positions to the 3′-end of two oligonucleotides. The 4-substituted
bis(terpyridine)Fe(II) complex orients two oligonucleotides at a 90° angle.
DNA strands A, B, and C are complementary to A′, B′, and C′, respectively.
The terpyridine and bis(terpyridine)Fe(II) complex X are shown in green,
and DNA strands are shown in red, yellow, and blue, respectively.
were prepared by adding two equivalents of Fe(II) ions to an
Scheme 2 a
a Reagents and conditions: (a) t-BuOK, O2, DMF, rt, 82%; (b) SOCl2,
MeOH, reflux, 77%; (c) NaBH4, THF/EtOH (10:1), 80 °C, 87%; (d)
Br(CH2)3OTBDMS, NaH, DMF, rt, 98%; (e) m-CPBA, CH2Cl2, rt, 83%;
(f) Bu4NF, THF, rt, 98%; (g) DMT-Cl, DMAP, pyridine, rt, 91%; (h) KCN,
DMF, 100 °C, 89%; (i) NaOH, H2O/MeOH/ethylene glycol, 85 °C, then
MeI, DMF, rt, 48%; (j) NaBH4, THF/EtOH (10:1), 85 °C, 70%; (k) (i)
succinic anhydride, DMAP, pyridine, rt, (ii) LCAA-CPG, HOBt, BOP,
DIEA, DMF, rt, then (iii) Ac2O, DMAP, CH2Cl2, rt, 28 µmol/g.
With 12 in hand, we set out to synthesize terpyridine-DNA
conjugates using automated methods. Each of these conjugates
contains a DNA strand tethered by its 3′-end to the 4-position of
terpyridine. Two-way branched metal-organic modules 13-17
† Korea University.
‡ Chung-Ang University.
9
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J. AM. CHEM. SOC. 2004, 126, 8606-8607
10.1021/ja048537q CCC: $27.50 © 2004 American Chemical Society

C O M M U N I C A T I O N S
This derivative affords terpyridine-DNA conjugates that serve as
a key building block to create molecular modules. These molecular
modules are easily generated by mixing terpyridine-DNA conju-
gates with metals and are successfully employed for the construction
of DNA triangles. Taken together, a bis(terpyridine)Fe(II) complex
demonstrates its potential for an alternative to the Holliday junction
in DNA-based self-assembly. Further study for the preparation of
terpyridine derivatives functionalizable with multiple oligonucle-
otides in a geometrically distinct way using solid-phase DNA
synthesis is in progress.
Acknowledgment. This work was financially supported by the
Korea Research Foundation Grant (KRF-2003-015-C00377). Fel-
lowship support from the BK21 and CRM programs (J.S.C.,
C.W.K., K.J., and J.W.Y.) is gratefully acknowledged.
Supporting Information Available: Detailed synthetic procedures
and characterization. This material is available free of charge via the
Internet at http://pubs.acs.org.
Figure 1. (Upper) Sequences of DNA strands A, B, and C and their
complementary oligonucleotides A′, B′, and C′ respectively linked to a
central bis(terpyridine)Fe(II) complex X in the modules 13-17. Two
complementary DNA strands a and a′ contain the reverse sequences of A
and A′, respectively. (Lower) Gel-shift analysis of the formation of DNA
triangles by PAGE on a 15% nondenaturing polyacrylamide gel.6 The
modules 13 and 14 were labeled with 32P at the 5′-end of DNA strands.
Each lane contains an equimolar mixture of component modules indicated
at the top.
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equimolar mixture of two different terpyridine-DNA conjugates
in H2O (Figure 1, Upper). Each of these modules contains a central
bis(terpyridine)Fe(II) complex X flanking two single-stranded
DNAs that differ in sequence and length. The sequences of DNA
strands A, B, and C in the modules are complementary to those of
A′, B′, and C′, respectively. As controls, two complementary DNA
strands a and a′ with reverse sequences of A and A′, respectively
were also synthesized. The length difference between two DNA
strands attached to a bis(terpyridine)Fe(II) complex allowed facile
separation of heterodimeric modules from homodimeric ones using
PAGE on a 20% denaturing polyacrylamide gel after they were
formed upon complexation of an Fe(II) metal ion by two terpyri-
dine-DNA conjugates.6 The relative orientation of two single-
stranded DNAs in each module is constrained at a 90° angle due
to their positioning on a bis(terpyridine)Fe(II) complex.
Triangular assembly of modules 13-17 was initiated simply by
annealing an equimolar mixture of the component modules in TE
buffer and thereby allowing intermodular DNA duplex formation
(Figure 1, Lower). Proper formation of DNA triangles was
confirmed by comparison with a control series of linear assemblies
on a 15% nondenaturing polyacrylamide gel.6 DNA triangles were
formed only when three modules were annealed such that the
sequence of each DNA strand in one module was complementary
to that in the other in a cyclic way (Figure 1, Lower, lanes 5 and
12). DNA triangles migrated more slowly than linear assemblies
despite the same length and sequence composition (Figure 1, Lower,
lanes 5, 12 vs 6, 11, respectively). DNA triangles appeared as a
single band, indicating that their structure is not destabilized by
the presence of bis(terpyridine)Fe(II) complex junctions. Formation
of significant quantities (>99%) of DNA triangles precluded the
presence of higher cyclic species. It is noteworthy that these
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about 48°, 58°, and 74° and side lengths of 17, 15, and 13 base
pairs in DNA triangles. Thus, DNA precisely placed three bis-
(terpyridine)Fe(II) complexes at nanoscale distances in triangular
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In conclusion, we describe the synthesis of a terpyridine
derivative that can be site-specifically linked to an oligonucleotide.
JA048537Q
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