Modular-DNA-Programmed Construction of Permanent Nanoscale Cyclic Assemblies by Reaction of Covalently linked 2,5-<i>bis</i>(2-Thienyl)pyrrole Monomers

Abstract

DNA modules that contain complementary recognition units and covalently linked 2,5-<i>bis</i>(2-thienyl)­pyrrole (SNS) monomers spontaneously assemble in aqueous buffer solution into cyclic structures. Ligation of the DNA modules is readily accomplished by an oxidative reaction with horseradish peroxidase (HRP)/H₂O₂, which results in covalent bond formation between the SNS monomers to form permanent nanoscale assemblies. The flexibility of the cyclic assemblies, and their ability to form SNS-to-SNS bonds, was assessed by varying the number and location of SNS monomers on each DNA module. Efficient ligation is observed when each module contains at least two SNS monomers. Ligation efficiency is diminished when the single stranded regions of the assembly are converted to duplex DNA. The efficient ligation of the DNA structures is attributed to the self-association of the monomers due to their hydrophobicity and is enabled by the flexibility of the single-stranded regions. It was found by systematically controlling the position and number of SNS monomers that these DNA modules are efficiently ligated into cyclic assemblies when each nucleobase module contains at least two SNS monomers. This provides a method for formation of unique covalently linked DNA structures and a process that can readily ligate or cross-link DNA chemically