Method for detecting single strand breaks in DNA

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

• fragmenting DNA with the SSBs to obtain fragmented DNA with available 3′ ends of the SSBs using a method that generates unavailable 3′ ends that cannot be tailed to generate fragmented DNA;
• adding a first tail to the available 3′ ends of the SSBs of the fragmented DNA 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 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 the positions of the SSBs through analysis of the sequencing results of the NGS.