Paranemic Crossover DNA: There and Back Again

Abstract

Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX, has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a 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. This review discusses the many attributes and usages of PX-DNA-its design, characteristics, applications, and potential biological relevance-and aims to accelerate the understanding of PX-DNA motif in its many roles and manifestations.

DNA Origami as Scaffolds for Self‐Assembly of Lipids and Proteins

“…To solve the structural instability and flexibility issues found in earlier DNA nanostructure assembly methods, Seeman and Fu constructed double crossover (DX) motifs as building blocks, in which a second strand exchange was introduced to make crossovers between two adjacent DNA helices, known as double Holliday junction structures, that constituted the foundation of structural DNA nanotechnology . In subsequent decades, many motifs have been developed for DNA nanotechnology, including triple crossover, paranemic crossover (PX), four‐stranded i‐motif, G‐quadruplexes, and other specific motifs . Furthermore, in addition to static hierarchical structures, dynamic nanomachines have also been achieved based on strand‐displacement reactions or configuration adjustment…”

Nuclease Degradation Analysis of DNA Nanostructures Using Gel Electrophoresis

“…In our recent research, we studied the biostability of a DNA motif called paranemic crossover (PX) DNA and explored the crossover-dependent biostability of DNA motifs by comparing PX DNA with similar motifs that contained lesser number of crossovers (Chandrasekaran et al, 2020). PX DNA is a four-stranded DNA structure that consists of two adjacent and connected double helical DNA domains (Shen et al, 2004;Wang et al, 2019) (Fig. 1).…”

“…Each duplex domain of PX DNA contains alternating major (wide) groove (denoted by W) or a minor (narrow) groove separation (denoted by N) flanking the central dyad axis of the structure, with one helical repeat containing a mixture of four half turns. In our study, we used a PX DNA motif with major/minor groove separations (W:N) of 6 and 5 nucleotides, respectively (Shen et al, 2004;Wang et al, 2019). Using gel-based analysis, we reported degradation times, kinetics of nuclease digestion, enzyme-specific concentration gradients on DNA motifs, and evaluation of biostability enhancement factors (Chandrasekaran et al, 2020).…”

Exceptional biostability of paranemic crossover (PX) DNA, crossover-dependent nuclease resistance, and implications for DNA nanotechnology

“…4 Another less common DNA motif is paranemic crossover (PX) DNA, a four-stranded DNA structure that consists of two adjacent and connected double helical DNA domains (Figure 1a). 9,10 The motif is formed by creating crossovers between strands of the same polarity at every possible point between two side-by-side helices. 10 Each duplex domain of PX DNA contains alternating major (wide) groove (denoted by W) or a minor (narrow) groove separation (denoted by N) flanking the central dyad axis of the structure, with one helical repeat containing a mixture of four half turns.…”

“…Previous studies have reported PX DNA with different major/minor groove separations (W:N), with the most stable complexes containing 6, 7 or 8 nucleotides in the major groove and 5 nucleotides in the minor groove (PX 6:5, 7:5 and 8:5 respectively). 9,10 In DNA nanotechnology, PX DNA has been used to construct objects such as an octahedron 11 and a triangle, 12 as well as one-and two-dimensional arrays. 13,14 PX DNA has also been a component of nanomechanical devices 15 that are used in molecular assembly lines 16 and DNA-based computation.…”