Bidirectional Control of Gold Nanoparticle Assembly by Turning On and Off DNA Hybridization with Thermally Degradable Molecular Glue

Hybridization of single-stranded DNA (ssDNA) with its complementary strand is important not only in many biological processes but also in DNA-based bioassays and nanodevices. The high sequence specificity of hybridization has also been applied to the construction of nanometer-scale structures and DNA-based molecular machines that include controlled motion of DNA. Modulation and control of the formation of double-stranded DNA (dsDNA) is a general strategy for enhancing, limiting, or triggering these biological processes and functions. Several methods have been reported for the control of DNA hybridization by using photochemical and electronic reactions on chemically modified DNA. We have introduced the concept of “molecular glue” for the mediation of hybridization of unmodified DNA with synthetic small molecules that bind to sequences containing up to three contiguous base mismatches. Molecular glue can adhere to two unmodified ssDNA molecules that do not hybridize with each other. The function of the molecular glue that we previously reported relied on thermodynamically favorable ligand binding to two ssDNA molecules. Its function did not include the denaturation of the duplex once formed, and was limited to the unidirectional control of DNA hybridization. To achieve bidirectional control, that is, to turn DNA hybridization on and off, we have looked for methods to inactivate the molecular glue in the reaction system. Here, we describe bidirectional control of DNA hybridization by using the new thermally degradable molecular glue, TD (Scheme 1). Irreversible thermal conversion of TD into its inactive form allowed us to control the DNA hybridization/denaturation cycle. This method for turning DNA hybridization on and off was then applied to the control of the assembly of gold nanoparticles. TD consists of two naphthyridine heterocycles that recognize guanine and selectively bind to dsDNA molecules with G– G mismatches. A key feature of TD, compared to the molecular glue previously reported, is its ability to function as a glue for DNA at room temperature but then be inactivated at an elevated temperature. In order to acquire inactivation, we modified the structure of the original molecule and found that, at an elevated temperature, the bond that connects the two naphthyridine heterocycles can be removed, which remarkably results in the inactivation of the glue function. Thermolysis of TD in 10 mm sodium cacodylate buffer (pH 7.0), as monitored by reversed-phase HPLC, showed that TD was completely consumed within 4 min incubation at 80 8C with concomitant formation of two products (Figure 1). The products were identified as 2-amino-7-methyl-1,8-naphthyridine (1) and (7methyl-1,8-naphthyridin-2-yl)-carbamic acid 2-(2-oxo-oxazolidin-3-yl)-ethyl ester (2 ; Figure 1B). The formation of 1 and 2 indicated that TD underwent thermal fragmentation by an intramolecular carbamate exchange. These results showed that TD could be irreversibly transformed to 1 and 2 by simple heating, and was therefore no longer effective in stabilizing dsDNA. The function of TD as a molecular glue for DNA was confirmed by measuring the melting temperature (Tm) of 11-mer duplexes (5’-d(CTAACXGAATG)-3’/5’-d(CATTCYGTTAG)-3’) that contained mismatches. Experiments were carried out with all possible combinations of matched and mismatched base pairs (represented by X–Y in the sequences) in the absence and presence of TD. TD selectively bound to the dsDNA that contained the G–G mismatch (X=Y=G; see the Supporting Information). In the presence of 100 mm TD, the Tm increase (DTm) for the duplex that contained the G–G mismatch was 25.7 8C; [a] Dr. T. Peng, Dr. C. Dohno, Prof. K. Nakatani Department of Regulatory Bioorganic Chemistry The Institute of Scientific and Industrial Research (SANKEN) Osaka University 8–1 Mihogaoka, Ibaraki 567-0047 (Japan) Fax: (+81)6-6879-8459 E-mail : nakatani@sanken.osaka-u.ac. jp Supporting information for this article is available on the WWW under http://www.chembiochem. org or from the author. Scheme 1. A) The structure of TD and its hydrogen-bonding pattern with guanines on opposing strands of a DNA duplex. B) Schematic representation of TD-assisted hybridization of two ssDNA molecules that contain the sequences 5’-XGG and 5’-XGG (X=C or T), and denaturation of TD-bound dsDNA by heat-induced inactivation of TD followed by gradual cooling to room temperature. The X bases in the XGG/XGG sequence are expected to be flipped-out of the helix, as shown on the right-hand side of the arrow.