Conformations of DNA in Triangular Nanochannels

Despite the widespread use of triangular nanochannels for the manipulation and analysis of DNA, studies on the confining effects induced by these nanofluidic structures on the molecules are still absent. Here, we perform coarse-grained Monte Carlo simulations to study the conformations of DNA in nanochannels. The influence of the shape of the nanochannel cross section is examined by comparing the elongation of molecules in triangular, rectangular, and square channels. Furthermore, the conformation of A-DNA under weak confinement is studied both computationally and experimentally. Good agreement between optical measurements and simulations supports the reliability of the numerical model in predicting the molecule conformation, making it a reliable method to obtain information essential in many applications, such as DNA barcoding.