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DNA melting in the presence of fluorescent intercalating oxazole yellow dyes measured with a gel‐based assay
Author(s) -
Bjorndal Michael T.,
Fygenson D. Kuchnir
Publication year - 2002
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10220
Subject(s) - intercalation (chemistry) , chemistry , dna , dimer , monomer , fluorescence , molecule , circular dichroism , oxazole , melting temperature , duplex (building) , crystallography , stereochemistry , photochemistry , polymer , organic chemistry , biochemistry , physics , materials science , quantum mechanics , composite material
We measured the effect of the intercalating oxazole yellow DNA dye quinolinium,4‐[(3‐methyl‐2(3H)‐benzoxazolylidene)methyl]‐1‐[3‐(trimethylammonio)propyl]‐,diiodide (YO‐PRO) and its homodimer (YOYO) on the melting of self‐complementary DNA duplexes using a gel‐based assay. The assay, which requires a self‐complementary DNA sequence, is independent of the optical properties of the molecules in solution. The melting temperature of the DNA is observed to increase in direct proportion to the number of occupied intercalation sites on the DNA, irrespective of whether the dye molecules are in monomer or dimer form. The increase is ∼ 2.5°C for each intercalation site occupied in the presence of 38 m M [Na + ], for dye/duplex ratios in which less than 1/5 of the available intercalation sites are occupied. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 40–44, 2002