Stepwise Strategy for One‐Pot Synthesis of Single‐Stranded DNA Rings from Multiple Short Fragments

• Published in: Chembiochem : a European journal of chemical biology 2021-03, Vol.22 (6), p.1005-1011
• Main Authors: Sui, Zhe, An, Ran, Komiyama, Makoto, Liang, Xingguo
• Format: Article
• Language: English
• Subjects: biosynthesis; Convergence; Deoxyribonucleic acid; DNA; DNA biosynthesis; Exonuclease; Fragments; ligases; Oligonucleotides; one-pot synthesis; Selectivity; sequential addition; single-stranded DNA rings; Splints; Synthesis
• ISSN: 1439-4227; 1439-7633
• DOI: 10.1002/cbic.202000738

Cyclic rings of single‐stranded (ss) DNA have various unique properties, but wider applications have been hampered by their poor availability. This paper reports a convenient one‐pot method in which these rings are efficiently synthesized by using T4 DNA ligase through convergent cyclization of easily available short DNA fragments. The key to the present method is to separate all the splint oligonucleotides into several sets, and add each set sequentially at an appropriate interval to the solutions containing all the short DNA fragments. Compared with simple one‐pot strategies involving simultaneous addition of all the splints at the beginning of the reaction, both the selectivity and the yields of target ssDNA rings are greatly improved. This convergent method is especially useful for preparing large‐sized rings that are otherwise hard to obtain. By starting from six short DNA fragments (71–82 nt), prepared by a DNA synthesizer, a ssDNA ring of 452‐nt size was synthesized in 35 mol % yield and in high selectivity. Satisfactorily pure DNA rings were obtainable simply by treating the crude products with exonuclease. One at a time, please: Large, circular, single‐stranded DNAs (up to 452‐nt sizes) have been efficiently prepared from multiple linear, single‐stranded short DNA fragments by using T4 DNA ligase through sequential addition of different sets of splints in a one‐pot reaction. The lengths of splints and the order of splint addition were optimized to obtain a satisfying yield of c‐ssDNA products. This method is convenient and practical, and benefits the development of DNA nanotechnology and bioscience.