http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

Biological surface science

A nanometre-scale pore in a solid-state membrane provides a new way of electronically probing the structure of single linear polymers, including those of biological interest in their native environments. Previous work with biological protein pores wide enough to let through and sense single-stranded DNA molecules demonstrates the power of using nanopores, but many future tasks and applications call for a robust solidstate pore whose nanometre-scale dimensions and properties may be selected, as one selects the lenses of a microscope. Here we demonstrate a solid-state nanopore microscope capable of observing individual molecules of double-stranded DNA and their folding behaviour. We discuss extensions of the nanopore microscope concept to alternative probing mechanisms and applications, including the study of molecular structure and sequencing.

/pdf/dna-molecules-and-configurations-in-a-solid-state-nanopore-3znflmb42h.pdf

DNA molecules and configurations in a solid-state nanopore microscope.

Single-molecule studies of DNA mechanics.

Multivalent interactions can be applied universally for a targeted strengthening of an interaction between different interfaces or molecules. The binding partners form cooperative, multiple receptor-ligand interactions that are based on individually weak, noncovalent bonds and are thus generally reversible. Hence, multi- and polyvalent interactions play a decisive role in biological systems for recognition, adhesion, and signal processes. The scientific and practical realization of this principle will be demonstrated by the development of simple artificial and theoretical models, from natural systems to functional, application-oriented systems. In a systematic review of scaffold architectures, the underlying effects and control options will be demonstrated, and suggestions will be given for designing effective multivalent binding systems, as well as for polyvalent therapeutics.

Multivalency as a chemical organization and action principle.

Properties of Biomolecules Measured from Atomic Force Microscope Images: A Review

Changes in the Elastic Properties of Cholinergic Synaptic Vesicles as Measured by Atomic Force Microscopy

DNA methyltransferases modify specific cytosines and adenines within 2-6 bp recognition sequences. We used scanning force microscopy and gel shift analysis to show that M.HhaI, a cytosine C-5 DNA methyltransferase, causes only a 2 degree bend upon binding its recognition site. Our results are consistent with prior crystallographic analysis showing that the enzyme stabilizes an extrahelical base while leaving the DNA duplex otherwise unperturbed. In contrast, similar analysis of M.EcoRI, an adenine N6 DNA methyltransferase, shows an average bend angle of approximately 52 degrees. This distortion of DNA conformation by M.EcoRI is shown to be important for sequence-specific binding.

https://www.pnas.org/content/pnas/93/15/7618.full.pdf

Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.

DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity.

The substructure and responses of individual 100-nm synaptic vesicles to osmotic stress have been probed with an atomic force microscope (AFM) operating in tapping mode. Cholinergic synaptic vesicles from the electric organ of Torpedo californica were imaged continuously as the osmolarity of the buffer was decreased. Vesicles in hyposmotic buffer lysed to form flat circular structures on the mica surface with a diameter about two times that of intact vesicles and a thickness of 7.2 +/- 1.7 nm, which can accommodate the lipid bilayer plus the internal proteoglycan. Images of intact vesicles in air reveal creases in the membrane surface. Phase mode AFM images of lysed vesicles in air show the presence of a material not seen on intact vesicles that might be intravesicular proteoglycan released from the membrane at very low osmotic and ionic strength.

Ricardo A. Garcia

Papers

Properties of Biomolecules Measured from Atomic Force Microscope Images: A Review

Changes in the Elastic Properties of Cholinergic Synaptic Vesicles as Measured by Atomic Force Microscopy

Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.

DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity.

Substructure and responses of cholinergic synaptic vesicles in the atomic force microscope.