Single Molecule Spectroscopic Determination of Lac Repressor-DNA Loop Conformation

¹ University of Maryland, College Park
² Kyoto University

^* To whom correspondence should be addressed. E-mail: jdkahn{at}umd.edu.

Submitted on May 31, 2005
Revised on July 11, 2005
Accepted on 19 July 2005

	Abstract

The E. coli lactose repressor protein (LacI) provides a classic model for understanding protein-induced DNA looping. LacI has a C-terminal 4-helix bundle tetramerization domain that may act as a flexible hinge. In previous work, several DNA constructs, each containing two lac operators bracketing a sequence-induced bend, were designed to stabilize different possible looping geometries. The resulting hyperstable LacI-DNA loops exist as both a compact "closed" form with a V-shaped repressor and also a more "open" form with an extended hinge. The "9C14" construct was of particular interest because footprinting, electrophoretic mobility shift, and ring closure experiments suggested that it forms both geometries. Previous fluorescence resonance energy transfer (FRET) measurements gave an efficiency of energy transfer, ET, of 70%, confirming the existence of a closed form. These measurements could not determine whether open form or intermediate geometries are populated, or the time scale of interconversion. We have now applied single-molecule FRET to Cy3, Cy5 double-labeled LacI-DNA loops diffusing freely in solution. By using multiple excitation wavelengths and by carefully examining the behavior of the zero-ET peak during titration with LacI, we show that the LacI-9C14 loop exists exclusively in a single closed form exhibiting essentially 100% ET.

Key Words: DNA looping, dual color excitation, excitation power dependence, fluorescence resonance energy transfer, hyperstable loop, triplet-state acceptor

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