Probing DNA-peptide interaction forces at the single-molecule level.

The versatility of chemical peptide synthesis combined with the high sensitivity of AFM single-molecule force spectroscopy allows us to investigate, quantify, and control molecular recognition processes (molecular nanotechnology), offering a tremendous potential in chemical biology.Single-molecule force spectroscopy experiments are able to detect fast intermediate transition states, details of the energy landscape, and structural changes, while avoiding multiple binding events that can occur under ensemble conditions. Dynamic force spectroscopy (DFS) is even able to provide data on the complex lifetime.

Molecular mechanisms and kinetics between DNA and DNA binding ligands.

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.

Solid phase synthesis of an amphiphilic peptide modified for immobilisation at the C-terminus.

The solid phase peptide synthesis (SPPS) of the amphiphilic peptide Ac-(Leu-Ala-Arg-Leu)(3)-linker, which is modified at the C-terminus with 1,8-diamino-3,6-dioxaoctane as linker moiety, has been investigated. Two different approaches that allow for the synthesis of C-terminally modified, side-chain protected peptides were examined. The solid phase peptide synthesis using aliphatic safety-catch resin followed by activation and aminolysis with the mono-Boc protected linker was compared with the synthesis on 1,8-diamino-3,6-dioxaoctane loaded 2-chlorotrityl resin.

Single molecule force spectroscopy on ligand-DNA complexes: from molecular binding mechanisms to biosensor applications.

Recent developments in single molecule force spectroscopy (SMFS) allow direct observation and measurements of forces that hold protein-DNA complexes together. Furthermore, the mechanics of double-stranded (ds) DNA molecules in the presence of small binding ligands can be detected. The results elucidate molecular binding mechanisms and open the way for ultra sensitive and powerful biosensor applications.

Identification of binding mechanisms in single molecule-DNA complexes.

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.