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Kinetics of ethidium's intercalation in packaged bacteriophage T7 DNA: Effects of DNA packing density
Author(s) -
Griess Gary A.,
Serwer Philip,
Kaushal Varsha,
Horowitz Paul M.
Publication year - 1986
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.360250713
Subject(s) - chemistry , intercalation (chemistry) , dna , reaction rate constant , kinetics , bacteriophage , binding constant , arrhenius equation , biophysics , microbiology and biotechnology , crystallography , binding site , biochemistry , escherichia coli , activation energy , biology , organic chemistry , physics , quantum mechanics , gene
Abstract The kinetics of ethidium's intercalative binding to DNA packaged in bacteriophage T7 and two T7 deletion mutants have been determined, using enhancement of fluorescence to quantitate binding. At a constant ethidium concentration, the results can be described as first‐order binding with two different rate constants, k 1 *(= k 1 + k −1 ) and k 2 *(= k 2 + k −2 ). The larger rate constant ( k 1 * ) was at least four orders of magnitude smaller than the comparable first‐order forward rate constant for binding to DNA released from its capsid. At 25°C values of k 1 *decreased as the amount of DNA packaged per internal volume increased. This latter observation indicates that the rate of ethidium's binding to packaged T7 DNA is limited by an event that occurs inside of the DNA‐containing region of T7, not by the crossing of T7 capsid's outer shell. Arrhenius plots of k M 1 *are biphasic, indicating a transition for packaged DNA at a temperature of 20°C. The data indicate that k 1 *s are limited by either sieving of ethidium during its passage through the packaged DNA or subsequent hindered intercalation.