Poly(N-isopropylacrylamide): experiment, theory and application

Optical approaches for observing the dynamics of single molecules have required pico- to nanomolar concentrations of fluorophore in order to isolate individual molecules. However, many biologically relevant processes occur at micromolar ligand concentrations, necessitating a reduction in the conventional observation volume by three orders of magnitude. We show that arrays of zero-mode waveguides consisting of subwavelength holes in a metal film provide a simple and highly parallel means for studying single-molecule dynamics at micromolar concentrations with microsecond temporal resolution. We present observations of DNA polymerase activity as an example of the effectiveness of zero-mode waveguides for performing single-molecule experiments at high concentrations.

/pdf/zero-mode-waveguides-for-single-molecule-analysis-at-high-1u8cepddlv.pdf

Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations

General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics-fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse.

/pdf/principles-of-protein-folding-a-perspective-from-simple-3k57kibqjs.pdf

Principles of protein folding--a perspective from simple exact models.

http://www.biophysik.physik.uni-muenchen.de/download/biopheinf/seminar/Schwille_1997_JACS.pdf

Dual-color fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution

XIAOTAO PAN,∗ CAILI AW,∗ YANAN DU,† HANRY YU†,‡ 7 and THORSTEN WOHLAND,∗,§ ∗Department of Chemistry, National University of Singapore, 9 3 Science Drive 3, Singapore 117543, Singapore †Institute of Bioengineering and Nanotechnology, A*STAR, 31 Biopolis Way, 11 The Nanos #04-01, Singapore 138669, Singapore ‡Department of Chemistry, National University of Singapore, 13 3 Science Drive 3, Singapore 117597, Singapore §chmwt@nus.edu.sg 15

Fluorescence correlation spectroscopy

Direct measurement of a distinct correlation function by fluorescence cross correlation.

Etude par diffusion lumineuse dynamique de la solubilisation du poly(N-isopropylacrylamide) dans l'eau par addition de laurylsulfate de sodium (SDS). L'agent de surface en faible concentration empeche l'agregation du polymere: le polymere forme une dispersion stable de globules effondres isoles (solubilisation intermoleculaire). A concentration en SDS plus elevee, on observe une transition globule-pelote (solubilisation intramoleculaire)

Intermolecular and intramolecular solubilization: Collapse and expansion of a polymer chain in surfactant solutions.

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Direct measurement of a distinct correlation function by fluorescence cross correlation.

Intermolecular and intramolecular solubilization: Collapse and expansion of a polymer chain in surfactant solutions.