Engineering Logic‐Gated i‐Motif/G‐Quadruplex (iG4) Hybrid Structures for DNA Nanotweezer‐Based Aptasensing

Abstract

AbstractGiven high levels of both K+ and H+ in the tumor microenvironment, G‐quadruplex (G4) and i‐motif can in principle be utilized as two cooperative modules to build logic‐gated DNA nanodevices for microenvironment recognition and targeting. Combined use of G4 and i‐motif in DNA nanoassemblies, however, usually causes the uncontrolled DNA aggregation. To address this trouble, we well design a novel i‐motif/G‐quadruplex (iG4) hybrid structure that integrates two four‐stranded DNA helices in a folding topology, with a parallel mini‐duplex flanking at the 5’ end to provide a binding site for fluorescent ligands. This design enables that the folded and lighting‐up DNA structure is favored by H+ and K+ together, consistent with a two‐input AND gate behavior. We then employ the iG4 structure to guide a DNA nanotweezer that is clamped by an altered split ATP aptamer, which brings a proximity effect contributing to the proper folding of iG4 in slightly acidic microenvironments and enables the sensitive detection of endogenous ATP in cancer cell lysates.