RETRACTED ARTICLE: Cooperative melting in caged dimers of rigid small molecule-DNA hybrids

Article abstract of DOI:10.1021/ja801572n

Rigid small-molecule DNA hybrids (rSMDHs) have been synthesized with three DNA strands attached to a rigid tris(phenylacetylene) core. When combined under dilute conditions, complementary rSMDHs form cage dimers that melt at >10 °C higher and much sharper than either unmodified DNA duplexes or rSMDH aggregates formed at higher concentrations. With a 2.97 average number of cooperative duplexes, these caged dimers constitute the first example of cooperative melting in well-defined DNA-small-molecule structures, demonstrating the important roles that local geometry and ion concentration play in the hybridization/dehybridization of DNA-based materials. Copyright

Full text of DOI:10.1021/ja801572n

Published on Web 07/03/2008
Cooperative Melting in Caged Dimers of Rigid Small Molecule-DNA Hybrids
Brian R. Stepp, Julianne M. Gibbs-Davis, Dorothea L. F. Koh, and SonBinh T. Nguyen*
Department of Chemistry and International Institute for Nanotechnology, Northwestern UniVersity,
2145 Sheridan Road, EVanston, Illinois 60208-3113
Received March 2, 2008; E-mail: stn@northwestern.edu
Over the past two decades, DNA hybrid materials have become
the materials of choice in the development of new strategies for genetic
detection,1 templated synthesis,2 programmed self-assembly,3 and
molecular computing.4 Hybridized mixtures of materials containing
multiple DNA strands, such as DNA-functionalized comb polymers5
and DNA-functionalized gold nanoparticles (GNPs),6 have notably
sharpened dehybridization, or melting, profiles compared to unmodified
DNA:DNA duplexes. This enhanced melting property can be used to
improve the selectivity for single-nucleotide polymorphisms (SNPs)
and has been attributed in one model to cooperative melting of
neighboring duplexes.7 This “neighboring-duplex” model proposes that
hybridization of complementary multi-DNA materials leads to a
network of interlinked DNA duplexes where the condensed ion cloud
around each DNA duplex can appreciably overlap with those of its
neighbors. Under these conditions, the coalesced ion cloud stabilizes
the duplexes, causing them to melt as a cooperatiVe unit in a switchlike
fashion.8 Such cooperative melting is predicted to be observable with
as few as 2-3 cooperative duplexes,9,10 beyond the limit of alternative
theories that ascribe sharp melting behavior to macroscopic phase
transition (see Supporting Information (SI) for details).11
To date, switch-like melting transitions have only been observed
for large polymer-DNA5,8 and GNP-DNA aggregates6 linked through
numerous DNA duplexes. Herein, we report the first observation of
cooperative melting in discrete DNA-hybrid structures where caged
dimers are formed from small molecule-DNA hybrids (SMDHs)
possessing only three DNA strands around a rigid (r) small-molecule
core (Figure 1, pathway a). This result demonstrates the important roles
that local geometry and ion concentration play in DNA hybridization/
dehybridization processes and points the way for designing new DNA-
based materials with enhanced recognition properties.
Our rSMDHs were designed with a rigid tris(phenylacetylene) core
that allows for the placement of exactly three DNA strands at 120°
intervals with a fixed distance from the central benzene. While these
Figure 1. Synthetic scheme for rSMDHs and possible hybridized structures
between rSMDH-A and rSMDH-B, with a digital image of a native PAGE gel
rSMDH cage dimers possess fewer DNA strands per structure than
the polymer-DNA and GNP-DNA hybrids, they exhibit similarly
sharpened melting transitions. When compared to unmodified DNA:
DNA duplexes, their melting temperatures (Tm) increased by >10 °C
and their transitions narrowed from >20 to 3 °C.
containing rSMDH materials: lane 1, A:B rSMDH caged dimers formed in
dilute solution; lane 2, purified nonhybridized rSMDH-A; lane 3, crude sample
of nonhybridized rSMHD-A showing a large percentage of cores with
incomplete DNA conjugation. Both the 1-arm and 2-arm functionalized
materials can be seen eluting faster than the fully conjugated rSMDH-A. Lane
4, A:B rSMDH aggregates formed in concentrated solution. While the
concentrated sample may have up to 50% of the dimer present (based on the
gel data, see also Figure SI-2), the observed melting is noncooperative.
Previous theoretical12 and experimental13 studies on the aggregation
behavior of complementary structures with three or more “arms”
surrounding a central hub found that A:B dimers tend to form when
the corresponding partners are combined in dilute solutions. Accord-
ingly, we expect that a dilute 1:1 mixture of rSMDH molecules
possessing complementary DNA strands, attached through the 5′
terminus, would result in caged dimers (Figure 1, pathway a). By
design, the rigid small-molecule core and short spacer sequences
consisting of six thymidine units (T6) would allow these dimers to
have all three duplexes approximately parallel to each other with 20-40
Å duplex center-duplex center distances, within the theoretical
distance necessary for ion-cloud overlap.9 In contrast, concentrated
samples are not expected to melt cooperatively as they should form
large aggregates (Figure 1, pathway b) with the ion clouds not in
parallel alignment.
Symmetric rSMDH materials were prepared by synthesizing the
initial DNA arm from the surface of a controlled porosity glass bead
(CPG), followed by addition of the small-molecule core 1 and coupling
of the two remaining DNA arms (Figure 1).13 Following removal from
the solid support, the crude rSMDH products were purified by size-
selective dialysis to give the desired triply functionalized rSMDHs.
Hybridized rSMDHs were formed by combining equimolar amounts
of two complementarily functionalized rSMDHs in phosphate buffer
at 50 °C, annealing the mixture at 50 °C for 5 min, and allowing the
mixture to cool to room temperature over 8 h. The melting profile of
the hybridized mixture was ascertained by heating the samples from
9
9628 J. AM. CHEM. SOC. 2008, 130, 9628–9629
10.1021/ja801572n CCC: $40.75
2008 American Chemical Society

C O M M U N I C A T I O N S
noteworthy that mixtures containing a high concentration of rSMDHs
did not exhibit an enhanced melting temperature (Table 1, cf. entries
2 and 4 vs 7), presumably due to the lack of multivalent interactions
between neighboring rSMDHs: on average each rSMDH is only linked
to another rSMDH through a single DNA duplex (see SI for details).
In conclusion, well-defined rSMDHs possessing three DNA strands
have been synthesized and used to form caged dimers in dilute
solutions. These caged dimers comprise the first discrete small
molecule-DNA hybrids that exhibit both switchlike dehybridization
properties and enhanced melting temperatures similar to aggregates
of DNA-modified gold nanoparticles6 and polymer-DNA hybrids.5
These results provide conclusive evidence to support the neighboring-
duplex model as a critical tool for understanding DNA hybridization/
dehybridization processes at the discrete molecular/supramolecular level
where phase-transition theory relying on aggregate formation/dissolu-
tion cannot be applied. It may also allow researchers to push the limits
in the design of the next generation of DNA-based materials to
maximize DNA’s natural recognition ability via precisely spaced and
finely tuned duplex interactions.
Figure 2. Melting curves for rSMDH:rSMDH hybridization mixtures at high
(3.80 µM) and low (0.38 µM) concentrations in saline buffer (10 mM PBS,
pH ) 7.0, 150 mM NaCl). (Inset) First derivatives of the melting curves.
Table 1. Melting Data for Unmodified DNA (DNA:DNA) and
rSMDH (rSMDH:rSMDH) Hybrids
Acknowledgment. We would like to thank Professor G. C. Schatz
and Dr. Tatiana Prytkova for helpful and informative discussions.
Financial support for this work was provided by the NSF (Grant EEC-
0647560 through the NSEC program) and the NIH (NCI 1U54
CA119341-01 through the CCNE program).
entry
hybridization mixture
[DNA] (µM)
[NaCl] (mM)a
Tm (°C)
fwhm (°C)
1
2
3
4
5
6
7
8
DNA:DNA
DNA:DNA
0.38
3.80
3.80
3.80
3.80
0.38
0.38
0.38
150
150
75
150
300
75
39.2
44.1
37.5
41.5
49.0
43.2
51.5
56.0
20.0
23.0
20.0
17.5
22.0
3.2
rSMDH:rSMDH
rSMDH:rSMDH
rSMDH:rSMDH
rSMDH:rSMDH
rSMDH:rSMDH
rSMDH:rSMDH
Supporting Information Available: Synthetic procedures and char-
acterization data for rigid small molecule-DNA hybrids; methods and data
for hybridization experiments. This material is available free of charge
via the Internet at http://pubs.acs.org.
150
300
2.0
3.7
a NaCl concentration in a 10-mM PBS buffer solution at 7.0 pH.
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(0.38 µM [DNA]) has a Tm of 52 °C and a fwhm (full width at half-
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