# nCas9-based method for rolling-circle DNA substrate generation

## TL;DR

This paper introduces a new method using nCas9 to create customizable rolling-circle DNA substrates for various DNA-related applications.

## Contribution

A novel nCas9-based method for generating rolling-circle DNA substrates with precise control over gap size and fork position.

## Key findings

- nCas9 can be programmed to create specific DNA fragments on an 18-kb plasmid.
- The method allows for the construction of DNA forks with controlled flap length and gap size.
- The generated substrates were successfully used in an in vitro single-molecule DNA replication assay.

## Abstract

Rolling-circle DNA replication is a DNA-duplication mechanism whereby circular DNA templates are continuously copied to produce long DNA products. It is widely used in molecular diagnostics, DNA sequencing, nanotechnology, and in vitro DNA replication studies. The efficiency of rolling-circle replication reaction heavily relies on the quality of the rolling-circle DNA template. Existing methods to create rolling-circle DNA substrates often rely on unique restriction sites and have limited control over replication fork topology and position. To address these limitations, we present a straightforward, customizable, and efficient strategy for producing rolling-circle DNA substrates with control over gap size and fork position. Our method relies on the use of nickase Cas9 (nCas9), which can be programmed to target specific DNA sequences using guide RNAs. In a one-pot reaction, we target nCas9 to four sites on an 18-kb plasmid to create 8–11-bp fragments. These fragments are removed and a flap oligo is ligated, to construct a fork with precisely controlled flap length and gap size. We demonstrate the application of this DNA substrate in an in vitro single-molecule rolling-circle DNA-replication assay. With our method, any plasmid DNA can be converted into a rolling-circle template, permitting generation of more physiologically-relevant DNA templates.