Coherent Quenching of a Fluorophore for the Design of a Highly Sensitive In‐Stem Molecular Beacon

Abstract

Excitonic interaction was utilized to design a highly sensitive in-stem molecular beacon (ISMB) in which both a fluorophore and a quencher on D-threoninols are incorporated as a pseudo base pair (see scheme; optimized combination with Cy3 and modified Methyl Red). Minimization of the difference between λmax of the fluorophore and quencher maximized quenching efficiency.