Table 1.

Variations of the alkaline CometChip

Type of Damage	Comet Assay Modifications	Description
Single-strand breaks	No modifications are necessary to detect strand breaks (and damage converted to strand breaks) under standard assay conditions.	Cells can be lysed immediately to assess levels of spontaneous damage or exposed to a DNA damaging agent and assessed following exposure.
Base Lesions	Enzyme incubations are performed after cell lysis and prior to electrophoresis. DNA nicks are created at sites of base lesions .	Base damage caused by ROS or UV exposure may not be readily detected using the comet assay. However, the presence of a damaged base can be revealed using enzymes that cleave the DNA at sites of damage (e.g., using DNA repair enzymes).17
Bulky Adducts	Co-exposing cells to HU/AraC traps NER repair intermediates,33,34 creating a persis- tent strand break that can be detected using the comet assay.35	DNA adducts, bases to which chemical moieties have been added, can be formed directly (e.g., cisplatin),36 or indirectly following metabolic activity (e.g., benzo[a]pyrene).37 Due to the short half-life of single-strand breaks during nucleotide excision repair (NER), the standard comet assay is not very sensitive to the presence of bulky lesions. Assay sensitivity can be improved by trapping NER intermediates with hydroxyurea (HU) and 1-β-D-arabinofuranosyl cytosine (AraC).
Cross-links	Prior to electrophoresis, exposing the DNA to irradiation38 (or another DNA damaging agent)39,40 creates additional breaks in the DNA. Migration of this damage is inhibited by the presence of cross-links.	Cross-links, such as those caused by chemotherapeutics (e.g., Mytomicin C)2,5 deter DNA migration, instead of enabling DNA migration. To reveal whether a compound induces cross-links, cells are exposed to agents that induce single-strand breaks, and the extent to which migration is deterred reveals the presence of interstrand cross-links.41,42