Topological Linkage of DNA Tiles Bonded by Paranemic Cohesion

Abstract

Catenation is the process by which cyclic strands are combined like the links of a chain, whereas knotting changes the linking properties of a single strand. In the cell, topoisomerases catalyzing strand passage operations enable the knotting and catenation of DNA so that single- or double-stranded segments can be passed through each other. Here, we use a system of closed DNA structures involving a paranemic motif, called PX-DNA, to bind double strands of DNA together. These PX-cohesive closed molecules contain complementary loops whose linking by Escherichia coli topoisomerase 1 (Topo 1) leads to various types of catenated and knotted structures. We were able to obtain specific DNA topological constructs by varying the lengths of the complementary tracts between the complementary loops. The formation of the structures was analyzed by denaturing gel electrophoresis, and the various topologies of the constructs were characterized using the program Knotilus.

Paranemic Crossover DNA: There and Back Again

“…Adapted with permission from ref . Copyright 2004 Macmillan Publishers Ltd. (b) PX cohesion of two circles A and B, followed by topo I treatment that interlocks the cohesive loops . Complementary loops are denoted by 1–1′ and 2–2′.…”

“…Paranemic crossover (PX) DNA is a unique four-stranded coaxial DNA motif. It contains a group of DNA complexes with different major-groove separations and has introduced a novel and unprecedented paradigm in DNA nanotechnology by serving as a central element for manufacturing state-of-the-art and programmable nanomechanical devices, − including an assembly line and a DNA computing system. , It has also been used for synthesizing nanostructures that span the range from individual objects , to one-dimensional (1D) − and 2D periodic arrays. , PX-DNA is a molecule that bridges DNA nanotechnology and biology and is the first designer/complex DNA motif that has been successfully replicated in vitro and in vivo, by use of naturally existing protein machinery. Beyond its contribution as a molecular building block to DNA nanotechnology and DNA computing, the PX-DNA motif has recently found a potential new role directly in basic biology, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes.…”

Programming molecular topologies from single-stranded nucleic acids

“…The programmability of nucleic acids 9 , 10 makes them excellent candidates to use for creating topological knots at a molecular level. Synthetic topological DNA nanostructures have previously been constructed by creating topological nodes based on B-form/Z-form double-stranded DNA (dsDNA) helices 11 – 14 , paranemic crossovers 15 , 16 , and DNA four-way junctions 17 . In contrast to the strategies that rely on the design of individual topological nodes and finding the appropriate DNA motifs/interactions with which to assemble such nodes, a different approach is to fold one long single-stranded DNA (ssDNA) chain into programmable topologies.…”

Nucleic Acid Nanostructures for Chemical and Biological Sensing

“…The main features of DNA — its inherent nanoscale dimensions and specific molecular recognition — make it a versatile nanoscale building block. Researchers have taken advantage of this to construct two‐ and three‐dimensional lattices, topologically‐linked arrays, nanomachines and nanodevices . The occurrence of different conformations of DNA depending on the ionic environment has also been used to construct devices based on conformational changes .…”