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

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.

Design of Modular G‐quadruplex Ligands

“…Several dimethylindolenine cyanine derivatives have been designed to stack on the terminal quartet of a G4 structure . Structural diversity is explored by synthesizing compounds with different methine length linkers (trimethine, compounds 103 and 104 ; pentamethine, compound 105 ) and different substituents on the indolenine rings and/or the meso ‐carbon atom of the polymethine bridge (Figure ).…”

“…[54] Several dimethylindolenine cyanine derivatives have been designed to stack on the terminal quartet of aG 4s tructure. [54,55] Structural diversity is explored by synthesizingc ompounds with different methine length linkers( trimethine,c ompounds 103 and 104;p entamethine, compound 105)a nd different substituents on the indolenine rings and/ort he mesocarbon atom of the polymethine bridge ( Figure 18). Trimethine cyanines 104 a and 104 e exhibit slightly more favorable G4 binding than pentamethine analogues 105 a and 105 d,w hile maintaining av ery low dsDNA affinity.R eplacing the cationic propyl(trimethylammonium) groups on both indolenine rings with ab utyl group (i.e.,c ompound 103 a)o rh ydrophobic pro-pylphenyl groups (i.e., compound 103 b)l eads to poor G4 ligands.T his suggests that the positive chargeo nt he substituents is crucial to maintain favorable electrostatic interactions with the quadruplex motif.…”

Exploration of Cyanine Compounds as Selective Inhibitors of Protein Arginine Methyltransferases: Synthesis and Biological Evaluation

“… 49 − 51 On the contrary, the dimethylindolium lost the double strand DNA ( ds DNA) binding ability probably because of steric hindrance in ligand–DNA interaction caused by the dimethyl moiety. 55 , 56 …”

Benz[c,d]indolium-containing Monomethine Cyanine Dyes: Synthesis and Photophysical Properties

“…Imaging of macromolecules such as DNA by staining with fluorescent compounds is of great interest, therefore, expanding the options of available probes is vital to several areas of research spanning from medical diagnostics to genomics [22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38]. The synthesis of low cost, easy to manipulate systems for fast analysis is required [8].…”