Search

Author(s): James B. Thompson (corresponding author) [1]; Johannes H. Kindt [1]; Barney Drake [1]; Helen G. Hansma [1]; Daniel E. Morse [2]; Paul K. Hansma [1] Despite centuries of work, [...]

Research has been conducted on the Pseudomonas putida unsaturated biofilms. The use of the atomic force microscopy in determining the surface morphology and adhesion forces of the desiccated biofilms is discussed.

Atomic force microscopy has been used to examine how the condensation of circular plasmid DNA molecules is affected by polylysine (PLL) and PLL-asialoorosomucoid. A sequence of conformational changes were seen in various types of condensed DNA structures as condensation progresses. Findings support the model for DNA condensation in which circular DNA molecules fold several times into shorter rods.

The three-dimensional structure and dynamic motion of laminin-1 molecules have been studied using atomic force microscopy. Laminins are extracellular matrix proteins that play a role in cell-matrix interactions that are significant in the movement and differentiation of cell types during development. Laminin-1 is the first laminin to be discovered and glycoprotein with three different polypeptide chains. A 400-kDa alpha chain, a 220-kDa beta chain and a 220-kDA delta chain.

The transcriptional activity of Escherichia coli RNA polymerase (RNAP), adsorbed on mica, is observed using tapping-mode atomic force microscopy (AFM). Sequential AFM images show unidirectional translocation of DNA template by RNAP on addition of ribonucleoside 5'-triphosphates (NTPs). An NTP concentration of five micro M is used to keep the rate of transcription low. The rate of transcription at this NTP concentration is 0.5 bases/s to two bases/s. The transcription rate is low due to the adsorption of RNAP on mica and exposure to Zn2+.

DNA conformations at the molecular level can be construed by visualizing individual DNA molecules using atomic force microscope (AFM). AFM reveals that tiny organic ligands can bend the DNA. A new ligand, MGT-6b, binds to DNA with its polyamine segment and tripyrrole peptide segment. The ligand has both bending and straightening properties as it binds DNA depending on DNA sequences.

The atomic force microscope can be used to forcibly unfold and extend single polypeptide chains. The resulting force versus distance curves have been widely interpreted to arise from the loss of entropy that the unfolded polypeptide chain experiences as it is extended. Here, we have used Monte Carlo simulations of unfolded polypeptide chains to examine the average distance between the ends of a polypeptide chain as a function of the force that pulls these ends apart. We examine two types of experiments: (a) A rigid force-sensor (bead-type) experiment: The chain is subjected to a constant stretching force f and the resulting chain extension is measured. (b) A flexible force-sensor (cantilever-type) experiment: The force is measured by the deflection of a cantilever that is attached to one end of the chain. The total length of the chain plus the displacement of the cantilever is fixed. In case (b), in the limit of a large cantilever force constant, the entropic force f is related to the free energy of the chain F(r) constrained to have the end-to-end distance r by the usual thermodynamic relationship: f=dF/dr. However in case (a) this relationship is invalid. The reason of its failure is that large fluctuations in the end-to-end distance r cannot be neglected at the single molecule level and so macroscopic thermodynamics relationships cannot be used. Thus the two types of experiments measure different force extension curves f(r). We compute the force extension curves for a model of a polypeptide chain in each case and find that they are significantly different. We further discuss implications of our findings with regard to the results of cantilever-type unfolding experiments. © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]