Molecular cooperativity of drebrin1-300 binding and structural remodeling of F-actin.

Drebrin A, an actin-binding protein, is a key regulatory element in synaptic plasticity of neuronal dendrites. Understanding how drebrin binds and remodels F-actin is important for a functional analysis of their interactions. Conventionally, molecular models for protein-protein interactions use binding parameters derived from bulk solution measurements with limited spatial resolution, and the inherent assumption of homogeneous binding sites.

Image analysis and length estimation of biomolecules using AFM.

There are many examples of problems in pattern analysis for which it is often possible to obtain systematic characterizations, if in addition a small number of useful features or parameters of the image are known a priori or can be estimated reasonably well. Often the relevant features of a particular pattern analysis problem are easy to enumerate, as when statistical structures of the patterns are well understood from the knowledge of the domain. We study a problem from molecular image analysis, where such a domain-dependent understanding may be lacking to some degree and the features must be inferred via machine-learning techniques.

Identifying individual DNA species in a complex mixture by precisely measuring the spacing between nicking restriction enzymes with atomic force microscope.

We discuss a novel atomic force microscope-based method for identifying individual short DNA molecules (<5000 bp) within a complex mixture by measuring the intra-molecular spacing of a few sequence-specific topographical labels in each molecule. Using this method, we accurately determined the relative abundance of individual DNA species in a 15-species mixture, with fewer than 100 copies per species sampled. To assess the scalability of our approach, we conducted a computer simulation, with realistic parameters, of the hypothetical problem of detecting abundance changes in individual gene transcripts between two single-cell human messenger RNA samples, each containing roughly 9000 species.

Localized nanoscopic surface measurements of nickel-modified mica for single-molecule DNA sequence sampling.

Cleaved, cation-derivatized Muscovite mica is utilized extensively in atomic force microscopy (AFM) imaging because of its flatness over large areas (millimeter cleavage planes with local root-mean-square roughness < 0.3 nm), ease of preparation, and ability to adsorb charged biomolecules such as DNA (work by Hansma and Laney, Guthold et al., and McMaster et al.

Nanocharacterization in dentistry.

About 80% of US adults have some form of dental disease. There are a variety of new dental products available, ranging from implants to oral hygiene products that rely on nanoscale properties. Here, the application of AFM (Atomic Force Microscopy) and optical interferometry to a range of dentistry issues, including characterization of dental enamel, oral bacteria, biofilms and the role of surface proteins in biochemical and nanomechanical properties of bacterial adhesins, is reviewed.

A breakthrough therapy for dentin hypersensitivity: how dental products containing 8% arginine and calcium carbonate work to deliver effective relief of sensitive teeth.

Objective: These studies have utilized a range of state-of-the-art surface techniques to gain insight into the mechanism of action of a new technology for dentin hypersensitivity relief based upon arginine and calcium carbonate and, in particular, to address important questions regarding the nature and extent of dentin tubule occlusion.

Methods: Confocal laser scanning microscopy (CLSM), scanning electron microscopy (SEM), and atomic force microscopy (AFM) have been used to assess tubule occlusion. Energy dispersive x-ray (EDX) and electron spectroscopy for chemical analysis (ESCA) have been used to identify the composition of the dentin plug.

Atomic force microscope observation of branching in single transcript molecules derived from human cardiac muscle.

We have used an atomic force microscope to examine a clinically derived sample of single-molecule gene transcripts, in the form of double-stranded cDNA, (c: complementary) obtained from human cardiac muscle without the use of polymerase chain reaction (PCR) amplification. We observed a log-normal distribution of transcript sizes, with most molecules being in the range of 0.4-7.