Progress toward “Click”-based Small-molecule DNA Hybrids Part II: Di- and Tri-functionalized Core

This paper reports the syntheses of acetylene-terminated smallmolecule cores. Also reported are successful attempts at “click” coupling the core molecules with azide-terminated oligonucleotides to construct stable small-molecule DNA hybrids (SMDH). Once these click-based small-molecule DNA hybrids are formed, melting studies will be done that study how the geometry of SMDH aggregate systems affects the suspected sharp melting transitions. Introduction As mentioned previously,1 efficient diagnosis of genetic diseases requires the development of detection assays that are both highly selective and sensitive. While several DNA detection systems recently have been developed based on the sharpened melting profile (compared with that of free DNA) exhibited by aggregated DNA hybrids (Figure 1), a complete description of the parameters that govern such sharp melting behavior has not been achieved.2 To this end, this study has designed small-molecule DNA hybrids (SMDHs) possessing fixed geometries and a number of DNA strands that can serve as an ideal model system for deciphering structure−property relationships in hybrid DNA materials. As the structure of SMDHs can be tuned in a modular fashion, the parameters that affect the observed sharp melting transitions can be unraveled systematically, enabling superior detection methods. Stepp and coworkers recently synthesized a three-armed SMDH with a rigid phenylacetylene core that is ideal for maintaining a fixed geometry between parallel DNA arms.3 While this SMDH exhibits sharp melting when treated with its complementary SMDH at a very dilute concentration, its low stability — a consequence of the labile benzylic phosphate-ester linkage between the core4 and the DNA arms — prohibited further studies. In addition, synthesizing these SMDHs is less than ideal for creating a diversity of core molecules; any variation of the intended core structure would require a significant reworking of the synthetic route. Hence, the researchers proposed the synthesis of triazole-linked SMDHs through the connection of azide-terminated DNA strands to acetylene-terminated small molecules using “click” chemistry (Figure 2).1 Stronger and more stable SMDHs can be produced by attaching DNA to rigid phenylacetylenebased core structures through a stable triazole linkage. In addition, the modular synthetic approach will ease diversification, thereby permitting a wide range of SMDH materials to be synthesized and studied — leading to the development of improved DNA detection systems. Previously, the authors reported the syntheses of two silyl-protected acetylene core molecules.1 This project extends this chemistry to two other cores and focuses on the click chemistry of coupling the acetyleneterminated cores with azide functionalized DNA.