Allosteric DNA molecular beacons: Using a novel mechanism to develop universal biosensor arrays to fully discriminate DNA/RNA analogues

Abstract

With a unique stem-loop hairpin structure, DNA molecular beacons have proven effective in the accurate discrimination of nucleic acid sequences with small changes. However, there are still many problems in current molecular beacons such as stringent assay conditions, insufficient specificity, non-universality and difficulty in multi-targets recognition. One universal type of allosteric DNA molecular beacons was developed in this work by separating the recognition element and signal reporter. The response process was demonstrated by real-time fluorescence simulations and native gel electrophoresis. Used as universal elements in biosensor arrays, the allosteric DNA molecular beacons can fully discriminate various muted DNA/RNA targets as separate clusters without any overlap. The new allosteric DNA molecular beacons have many advantages over conventional ones, typically used for biosensor arrays, and expand the application prospect of molecular beacons for complex bioassay tasks.