Selective G-Quadruplex DNA Recognition by a New Class of Designed Cyanines

Rupesh Nanjunda,Ekaterina Stroeva,W Wilson,Tyler Dost,Eric Owens,Maged Henary,Leah Mickelson,Hang Huynh,Markus Germann

doi:10.3390/molecules181113588

Abstract

A variety of cyanines provide versatile and sensitive agents acting as DNA stains and sensors and have been structurally modified to bind in the DNA minor groove in a sequence dependent manner. Similarly, we are developing a new set of cyanines that have been designed to achieve highly selective binding to DNA G-quadruplexes with much weaker binding to DNA duplexes. A systematic set of structurally analogous trimethine cyanines has been synthesized and evaluated for quadruplex targeting. The results reveal that elevated quadruplex binding and specificity are highly sensitive to the polymethine chain length, heterocyclic structure and intrinsic charge of the compound. Biophysical experiments show that the compounds display significant selectivity for quadruplex binding with a higher preference for parallel stranded quadruplexes, such as cMYC. NMR studies revealed the primary binding through an end-stacking mode and SPR studies showed the strongest compounds have primary KD values below 100 nM that are nearly 100-fold weaker for duplexes. The high selectivity of these newly designed trimethine cyanines for quadruplexes as well as their ability to discriminate between different quadruplexes are extremely promising features to develop them as novel probes for targeting quadruplexes in vivo.

Highlights

G-quadruplexes are higher order DNA structures formed by either intra- or intermolecular association of guanine-rich sequences into a stacked array of G-tetrads and stabilized by Hoogsteen hydrogen bonds as well as coordinated monovalent cations [1,2]
Preliminary Thermal Melting Screening (Tm) analysis of a synthetic set of symmetric trimethine cyanines containing different substituents on the indolenine rings (Figure 1) were conducted with a well-characterized telomeric quadruplex sequence (Tel22) and a control hairpin duplex sequence (AATT) that is quite favorable for detection of either minor groove or intercalative binding to duplexes
In accordance with the design principles established in the previous studies to enhance quadruplex interactions by halogenation of cyanines, systematic halogen substitutions on the indolenine rings in the current trimethine series showed a highly favorable increase in the thermal stability of the telomeric quadruplex (Table 1, compounds 29–32)

Summary

Introduction

G-quadruplexes are higher order DNA structures formed by either intra- or intermolecular association of guanine-rich sequences into a stacked array of G-tetrads and stabilized by Hoogsteen hydrogen bonds as well as coordinated monovalent cations [1,2]. A wide range of quadruplex-specific small molecules have been reported so far with some compounds showing very promising biological activities [9,10,11]. The synthetic ability to structurally tailor cyanines as well as their many therapeutically favorable features, such as low toxicity, renders them ideal candidates for their potential development as quadruplex targeting agents. The highly promising results of the pentamethine cyanines as quadruplex specific agents encouraged us to further explore the conformational space of cyanine molecules for increased quadruplex affinity and selectivity. The results are highly promising and encouraging towards the development of cyanine-based small molecules as highly specific quadruplex targeting agents

Results

Discussion

Conclusion