A Gold Nanoparticle-Based Approach for Screening Triplex DNA Binders

Abstract

Regulating gene expression by controlling nucleic acid transcription is a potential strategy for the treatment of genetic-based diseases. A promising approach involves the use of triplex-forming oligonucleotides (TFOs) [1]. Triple helix nucleic acids, or triplex structures, are formed through sequence-specific Hoogsteen, or reverse Hoogsteen, hydrogen bond formation between a single-stranded TFO and purine bases in the major groove of a target duplex [2]. Because TFOs can achieve sequence-specific recognition of genomic DNA, they can, in principle, be used to modulate gene 1544expression by interfering with transcription factors that bind to DNA. However, at present, only purine-rich sequences can be targeted, and the resultant triplex structure is less stable than the analogous duplex. This inherent instability has prompted research efforts to develop molecules that selectively bind to such triplex structures to stabilize the TFO-duplex complex. Potentially, triplex-specific binding molecules could be used in conjunction with TFOs to achieve control of gene expression [3]. Molecules identified as triplex binders include benzoindoloquinoline, benzopyridoquinoxaline, naphthyquinoline, acridine, and anthraquinone derivatives [4]. In the past, typical screening processes for identifying triplex binders have included competitive dialysis, mass spectroscopy, electrophoresis, and UV-vis melting experiments, most of which are not applicable to high-throughput screening processes [5]. However, with the development of combinatorial libraries which can produce large numbers of potential drug candidates, high-throughput screening strategies have become a necessary part of drug development [6].