DNA binding interactions Flashcards
how does EtBr affect DNA?
changes the 36 degree per turn to 10 degree per turn–more unwound; a saturated molecule is 27% ; EtBr can cause unbound regions to positively supercoil; during DNA replication, stretched DNA more likely to have frameshift mutation
Anthracycline general info
intercalating drug; intercalates bw alternating pur-pyr bases; planar, derived from natural antibiotics produced from Streptomyces; selective toxicity against rapidly-proliferating cells
what is danourubicin?
first anthracycline drug
how was anthracycline used therapeutically?
used as an anti-cancer drug; interferes with DNA replication & transcription: topoisomerase II and free radical production
what are the minor groove binders?
spermine–stabilizes DNA; netropsin–antibiotic; distamycin A–anticancer; Hoescht 33258–fluorescent stain; DAPI–fluorescent stain
netropsin general info
has high affinity for AT rich tetrameric sequences; binds to minor groove, high affinity for DNA prevents binding of DNA topoisomerase
Hoescht stain general info
bind minor groove; can be used as nuclear stains; give double the fluorescence in AT rich seqs than GC; also good because they are less toxic and can be used to visualize living cells
how can hoescht stain be used to isolate stem cells?
Hoescht dye 33342 is pumped out of the cytoplasm of hematopoietic stem cells into the nucleus faster than other RBCs; if it’s pumped out quickly, therefore there is more time for the Hoescht stain to bind to DNA–>gives off/absorbs more blue light, therefore there will be a higher blue:red ratio–>can plot all cell absorbances on a graph and see where their is a cluster of cells (“events”)
how and where does mustargen bind to DNA?
mustargen loses a Cl ion, produces cycle ethyleneimmonium which is very reactive–tends to react with the N7 of guanine (as well as other places)
what happens to alkylated guanine?
can be depurinated–>leads to DNA breakage; cross-stranded: linking of G–alkylating agent–G; mispairs with thymine
