Mechanical properties of single double-stranded DNA (dsDNA) in the presence of different binding ligands were analyzed in optical-tweezers experiments with subpiconewton force resolution. The binding of ligands to DNA changes the overall mechanic response of the dsDNA molecule. This fundamental property can be used for discrimination and identification of different binding modes and, furthermore, may be relevant for various processes like nucleosome packing or applications like cancer therapy. We compared the effects of the minor groove binder distamycin-A, a major groove binding alpha-helical peptide, the intercalators ethidium bromide, YO-1, and daunomycin as well as the bisintercalator YOYO-1 on lambda-DNA. Binding of molecules to the minor and major groove of dsDNA induces distinct changes in the molecular elasticity compared to the free dsDNA detectable as a shift of the overstretching transition to higher forces. Intercalating molecules affect the molecular mechanics by a complete disappearance of the B-S transition and an associated increase in molecular contour length. Significant force hysteresis effects occurring during stretching/relaxation cycles with velocities>10 nm/s for YOYO-1 and >1000 nm/s for daunomycin. These indicate structural changes in the timescale of minutes for the YOYO-DNA and of seconds for the daunomycin-DNA complexes, respectively.

In supramolecular chemistry [1] synthetically designed organic constituents interact noncovalently, in a directed and specific way to form host-guest complexes of higher complexity. The ability to tailor the molecular interplay with respect of chemical design, specificity, and molecular switching opens up the development of new molecular materials for artificial molecular recognition, molecular organization, and selfassembly. We have used mechanical single-molecule force spectroscopy to investigate the binding of individual resorc-[4]arene-ligand host-guest complexes. By using diluted samples of the host and guest molecules that are modified with a long linker which is attached to an atomic force microscope (AFM) tip, we were able to prevent multiple binding and to observe single host-guest unbinding events in a supramolecular system for the first time. The molecular binding forces, their dependence on external loading rates, the rate of dissociation, and the molecular cavity length directly relate to the molecular properties of the supramolecular species and are consistent with an activated decay of a metastable bound state, a finding already established for biological receptor-ligand complexes. This result allows new insights into the mechanisms, kinetics, and thermodynamics of intermolecular association in chemistry and biology, and opens new possibilities in the investigation, design, and development of synthetic receptor systems.Calixarenes are model receptor systems providing synthetic receptor cavities for the inclusion of small cationic guests, such as alkali-metal or ammonium ions. [2][3][4][5] Organic cations, such as ammonium ions, play a significant role in molecular recognition processes in nature (e.g. in protein side chains). Calix[n]arenes, generally, are a class of macrocyclic compounds formed by the base-catalyzed condensation of nphenol derivatives and formaldehyde. [2,3] The resorc [4]arenes [6,7] considered herein are calixarenes formed from four

We show that the standard theoretical framework in single-molecule force spectroscopy has to be extended to consistently describe the experimental findings. The basic amendment is to take into account heterogeneity of the chemical bonds via random variations of the force-dependent dissociation rates. This results in a very good agreement between theory and rupture data from several different experiments.

Changes in the elastic properties of single deoxyribonucleic acid (DNA) molecules in the presence of different DNA-binding agents are identified using atomic force microscope single molecule force spectroscopy. We investigated the binding of poly(dG-dC) dsDNA with the minor groove binder distamycin A, two supposed major groove binders, an alpha-helical and a 3(10)-helical peptide, the intercalants daunomycin, ethidium bromide and YO, and the bis-intercalant YOYO. Characteristic mechanical fingerprints in the overstretching behavior of the studied single DNA-ligand complexes were observed allowing the distinction between different binding modes. Docking of ligands to the minor or major groove of DNA has the effect that the intramolecular B-S transition remains visible as a distinct plateau in the force-extension trace. By contrast, intercalation of small molecules into the double helix is characterized by the vanishing of the B-S plateau. These findings lead to the conclusion that atomic force microscope force spectroscopy can be regarded as a single molecule biosensor and is a potent tool for the characterization of binding motives of small ligands to DNA.

A simple treatment based on continuum mechanics shows that weak interlamellar forces in crystalline n‐alkanes should result in a characteristic upward shift of the frequencies of the longitudinal acoustical (LA) modes, which is independent of the chain length and decreases inversely with the mode order. A raman spectroscopic determination of the LA mode frequencies of a series of different n‐alkanes confirms the theoretical conclusion and permits a derivation of a force constant characteristic of the interlamellar forces. The discussion results in a new formula valid for the LA mode frequencies of the orthorhombic n‐alkanes in the acoustical limit and yields a new determination of the limiting elastic modulus Ec of crystalline polyethylene. The value obtained, Ec = 2.9 × 1012 dyne/cm2, is markedly smaller than the value derived by Schaufele and Shimanouchi neglecting the influence of the interlamellar forces on the LA mode frequencies.