Method for detecting single strand breaks in dna

A method for detecting single strand breaks (SSBs) in deoxyribonucleic acid (DNA) comprising:

• fragmenting DNA to be tested with a method that generates 3′ ends that cannot be tailed to generate fragmented DNA;
• adding a first tail to available 3′ ends of SSBs of the fragmented DNA corresponding to tag endogenous breaks to generate tailed fragments;
• and
• capturing and identifying positions of the SSBs genome-wide, wherein the capturing and identifying comprises:
• linearly amplifying the tailed fragments using cycles of primer extension with a chimeric 5′-DNA-RNA-3′ primer;
• adding a second tail to 3′ ends of the products of the primer extension to obtain desired products;
• amplifying the desired products by a polymerase chain reaction (PCR) with oligonucleotides comprising adaptor sequences complementary to both the first tail and the second tail and subjecting to next-generation sequencing (NGS) to generate sequencing results;
• and
• revealing positions of the SSBs through analysis of sequencing results of the NGS.