DNA Conformational Regulation in PDMS Chambers under Low-Concentration Monovalent Ionic Solutions

Low concentrations of monovalent alkali metal ions fail to effectively shield the strong electrostatic repulsion between DNA strands, preventing them from approaching and forming entangled structures. This concentration dilemma limits the application of DNA entanglement-dependent programmable assembly strategies in physiologically relevant low-salt environments. To address this challenge, a PDMS chamber with spatiotemporal regulation capabilities was designed, featuring the following. (1) Spatial regulation: The PDMS evaporation chamber suppressed excessive lateral spreading behavior of droplets, thereby preventing nonuniform dispersion and rapid deposition of DNA and ions. Raman results indicated about 18-fold Na+ concentration enhancement in evaporation-driven droplets within PDMS chambers before liquid film rupture. (2) Temporal regulation: The liquid phase retention time of a 10 μL droplet was extended to 55–60 min under controlled conditions (22 °C, 55% RH), providing a temporal window for ion-mediated DNA conformational regulation. (3) DNA conformational regulation: Raman analysis revealed that the high-salt microenvironment formed by evaporative concentration in PDMS chambers drove the entanglement of DNA molecules. Atomic force microscopy (AFM) topographies further confirmed denser DNA entanglement networks in PDMS-chambered droplets, with higher surface coverage than those in open-surface droplets. This work presents a strategy for low-concentration monovalent-ion-mediated DNA morphological regulation, with potential applications in microfluidics, biosensing, and programmable nanomaterials.