Molecular Mechanisms and Kinetics between DNA and DNA Binding Ligands

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Presentation transcript:

Molecular Mechanisms and Kinetics between DNA and DNA Binding Ligands Andy Sischka, Katja Toensing, Rainer Eckel, Sven David Wilking, Norbert Sewald, Robert Ros, Dario Anselmetti Biophysical Journal Volume 88, Issue 1, Pages 404-411 (January 2005) DOI: 10.1529/biophysj.103.036293 Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 1 Single λ-phage DNA molecule and λ-DNA molecule complexed with minor groove binder (distamycin-A), major groove binder (α-helical peptide Ac-(Leu-Ala-Arg-Leu)3-NH-linker), intercalators (daunomycin, YO-1, ethidium bromide), and bisintercalator (YOYO-1), respectively, exhibit different elasticity curves indicating individual mechanical properties (force fingerprints). Total concentration of each binding ligand was 1μM, and stretching velocity was 100nm/s. (Inset) Worm-like-chain model fit on a free λ-DNA in the low-force regime up to 10pN. Biophysical Journal 2005 88, 404-411DOI: (10.1529/biophysj.103.036293) Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 2 (A) Force-extension curves of a single λ-phage DNA molecule and in the presence of DNA intercalator daunomycin (1μM) obtained at a stretching velocity of 100nm/s. (B) At higher velocities, daunomycin intercalated DNA reveals distinct hysteresis effects during extension relaxation cycles. Biophysical Journal 2005 88, 404-411DOI: (10.1529/biophysj.103.036293) Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 3 (A) YOYO-1 (1μM) bisintercalated λ-phage DNA molecule reveals hysteresis effects during extension/relaxation loop even at low stretching and relaxing velocities. (B) At increased velocities, elasticity curves are shifted to lower extension values. (C) Hysteresis effects at different maximum forces during stretching/relaxation loops of YOYO-1 bisintercalated λ-phage DNA. Biophysical Journal 2005 88, 404-411DOI: (10.1529/biophysj.103.036293) Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 4 (A) Fast stretching of YOYO-1 bisintercalated and daunomycin intercalated λ-phage DNA with a velocity of 5000nm/s and 12,000nm/s, respectively, to a maximum force and immediate stopping unveils an exponential decay of the retention force with time. (B) Percentage of exponential decay of the retention force as a function of maximum retention force for YOYO-1 and daunomycin. (C) Relaxation time as a function of maximum retention force for YOYO-1 and daunomycin. Due to high-extension velocity for daunomcin, short-time data acquisition implicates less data averaging, which effects more statistical noise and larger error bars. Biophysical Journal 2005 88, 404-411DOI: (10.1529/biophysj.103.036293) Copyright © 2005 The Biophysical Society Terms and Conditions