Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane

Qi Li,Sheng Liu,Makoto Komiyama,Yixiao Cui,Ran An,Jing Li,Xingguo Liang

doi:10.3390/molecules23092270

Abstract

DNA catenanes are characterized by their flexible and dynamic motions and have been regarded as one of the key players in sophisticated DNA-based molecular machines. There, the linking number (Lk) between adjacent interlocked rings is one of the most critical factors, since it governs the feasibility of dynamic motions. However, there has been no established way to synthesize catenanes in which Lk is controlled to a predetermined value. This paper reports a new methodology to selectively synthesize Lk 1 catenanes composed of single-stranded DNA rings, in which these rings can most freely rotate each other due to minimal inter-ring interactions. To the mixture for the synthesis, two holder strands (oligonucleotides of 18–46 nt) were added, and the structure of the quasi-catenane intermediate was interlocked through Watson–Crick base pairings into a favorable conformation for Lk 1 catenation. The length of the complementary part between the two quasi-rings was kept at 10 bp or shorter. Under these steric constraints, two quasi-rings were cyclized with the use of T4 DNA ligase. By this simple procedure, the formation of undesired topoisomers (Lk ≥ 2) was almost completely inhibited, and Lk 1 catenane was selectively prepared in high yield up to 70 mole%. These Lk 1 catenanes have high potentials as dynamic parts for versatile DNA architectures.

Highlights

Since the pioneering proposal by Seeman [1], a number of DNA nanoarchitectures have been elegantly constructed [2,3,4,5,6]
Xiu-juan et al used a strand displacement paradigm to trigger the switchable transition of a DNA catenane across three stations as a DNA rotor [16]
We developed a more advanced method in which linking number (Lk) 1 catenanes are selectively formed in high yields (e.g., 70 mole%)

Summary

Introduction

Since the pioneering proposal by Seeman [1], a number of DNA nanoarchitectures have been elegantly constructed [2,3,4,5,6]. DNA catenanes are highly unique and show specific properties which cannot be accomplished by other molecular assemblies Their most significant advantage is their structural flexibility and dynamic features. Their component rings are interlocked by a “mechanical bond” without any covalent linkages so that they can mutually rotate each other [7,8,9]. Their topological specificity is favorable to design highly complicated and sophisticated nanoarchitectures [10,11,12,13,14,15]. Xiu-juan et al used a strand displacement paradigm to trigger the switchable transition of a DNA catenane across three stations as a DNA rotor [16]

Methods

Results

Conclusion