Title
A 5′-BODIPY End-label for Monitoring DNA Duplex-Quadruplex Exchange
Author
Prashant S. Deore, Dmitriy V. Soldatov, Richard A. Manderville
Year
2018
Journal
Scientific Reports
Abstract
Fluorescent probes that can distinguish different DNA topologies through changes in optical readout are sought after for DNA-based diagnostics. In this work, the 4,4-difluoro-4-bora-3a, 4a-diaza-s-indacene (BODIPY) chromophore attached to cyanophenyl substituents (BODIPY-CN) has been tethered to the 5′-end of the 15-mer thrombin binding aptamer (TBA) that contains the guanine (G) nucleobase. TBA folds into a unimolecular antiparallel G-quadruplex (GQ) upon binding thrombin and certain metal ions. The 5′-BODIPY-CN-TBA sample possesses a Stokes shift of ~40 nm with wavelengths of excitation/emission at 550/590 nm and exhibits a 2-fold increase in emission intensity compared to the free BODIPY-CN in aqueous buffer that possesses a brightness (εΦfl) of ~16,956 M−1. cm−1. However, when 5′-BODIPY-CN-TBA is base-paired to a complementary strand in the B-form duplex, the emission of the BODIPY-CN end-label increases 7-fold, 14-fold compared to the free-dye. This signal-on response enables the BODIPY-CN end-label to serve as a quencher-free fluorescent probe for monitoring duplex-GQ exchange. The visible end-label minimally perturbs GQ stability and thrombin binding affinity, and the modified TBA can act as a combinatorial logic circuit having INHIBIT logic functions. These attributes make BODIPY-CN a highly useful end-label for creating nanomolecular devices derived from G-rich oligonucleotides.
Full Article
Instrument
J-815
Keywords
Circular dichroism, DNA structure, Chemical stability, Biochemistry