Low- and High-Resolution Mapping of DNA Damage at Specific Sites

• Published in: Methods (San Diego, Calif.) Calif.), 2000-10, Vol.22 (2), p.170-179
• Main Authors: Li, Shisheng, Waters, Raymond, Smerdon, Michael J.
• Format: Article
• Language: English
• Subjects: Biotinylation; Cell Division; Chromatin - chemistry; DNA Damage; DNA Mutational Analysis - methods; DNA Repair; Electrophoresis; Endodeoxyribonucleases - metabolism; Escherichia coli - genetics; Gene Expression; Genetic Markers; Multienzyme Complexes - metabolism; N-Glycosyl Hydrolases - metabolism; Plasmids - metabolism; Protein Structure, Tertiary; Restriction Mapping; Software; Streptavidin - metabolism; Ultraviolet Rays; Yeasts - genetics
• ISSN: 1046-2023; 1095-9130
• DOI: 10.1006/meth.2000.1058

Measurement of DNA damage and repair at the nucleotide level in intact cells has provided compelling evidence for the molecular details of these events as they occur in intact organisms. Furthermore, these measurements give the most accurate picture of the rates of repair in different structural domains of DNA in chromatin. In this report, we describe two methods currently used in our laboratories to map DNA lesions at (or near) nucleotide resolution in yeast cells. The low-resolution method couples damage-specific strand breaks in DNA with indirect end-labeling to measure DNA lesions over a span of 1.5 to 2 kb of DNA sequence. The resolution of this method is limited by the resolution of DNA length measurements on alkaline agarose gels (about ±20 bp on average). The high-resolution method uses streptavidin magnetic beads and special biotinylated oligonucleotides to facilitate end-labeling of DNA fragments specifically cleaved at damage sites. The latter method maps DNA damage sites at nucleotide resolution over a shorter distance (