Biomedical subjects

Ronald G Larson

Publications and source records attributed to Ronald G Larson.

26 records · Page 2Linked to original sources

PubMed2004

Preparation of fluorescent particles with long excitation and emission wavelengths dispersible in organic solvents.

We introduce a fast and simple one-step method, a variation of the methods of Barrett and Campbell and Bartlett, to synthesize monodisperse fluorescent particles that can be dispersed in organic solvents and have long excitation (649 nm) and emission wavelengths (679 nm). A lipophilic fluorescent dye, 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine perchlorate, is directly incorporated into PMMA particles through dispersion polymerization. A poly(hydroxystearic acid) graft (poly) methyl methacrylate (MM) and methacrylic acid (MA) copolymer is used as a stabilizer to prevent the particles from aggregating and flocculating in the nonaqueous solvents. The fluorescent PMMA particles are very uniform in size, bleach at very low rate, and behave like hard spheres in their ordering on substrates. One important achievement in our synthesis protocol is that we are able to produce particles of a desired size by choosing the composition of the reactants according to a predetermined relationship between particle size and composition of reactants. In addition, the effects of fluorescent dye and polar solvent (ethanol) on the formation and size of particles are discussed.

Biocompatible Materials↗

PubMed2004

Distribution of single DNA molecule electrophoretic mobilities in semidilute and dilute hydroxyethylcellulose solutions.

The distribution of center of mass electrophoretic mobility mobilities and normalized migration time of up to 1080 lambda DNA molecules per experiment were measured in both semidilute hydroxyethylcellulose HEC/0.5 x Tris-borate-EDTA (TBE) solutions and dilute HEC/0.5 x TBE solution by high-speed video microscopy. Measurements were made microscopically over a short migration distance in homogeneous DNA HEC/0.5 x TBE solution and after electrophoretic migration of a plug of DNA through 7 cm. Video at 120 frames/s (semidilute HEC solution) and 236 frames/s (dilute HEC solution) allowed visualization with adequate resolution for single molecule mobility measurements. The electrophoretic migration times and band shapes predicted from the measurements corresponded well with those measured by conventional capillary electrophoresis (CE) in both semidilute and dilute HEC. In semidilute solution, the band width predicted by a square root of time scaling is in good agreement with the results of conventional CE. However, in dilute solution the precision of the measurements was not good enough to allow scaled estimates of band widths.

Cellulose↗

PubMed2004

Binding and insertion of alpha-helical anti-microbial peptides in POPC bilayers studied by molecular dynamics simulations.

We have performed molecular dynamics simulations of the interactions of two alpha-helical anti-microbial peptides, magainin2 and its synthetic analog of MSI-78, with palmitoyl-oleoyl-phosphatidylcholine (POPC) lipid bilayers. We used various initial positions and orientations of the peptide with respect to the lipid bilayer, including a surface-bound state parallel to the interface, a trans-membrane state, and a partially inserted state. Our 20 ns long simulations show that both magainin2 and MSI-78 are most stable in the lipid environment, with the peptide destabilized to different extents in both aqueous and lipid/water interfacial environments. We found that there are strong specific interactions between the lysine residues of the peptides and the lipid head-group regions. MSI-78, owing to its large number of lysines, shows better binding characteristics and overall stability when compared to magainin2. We also find that both peptides destabilize the bilayer environment, as observed by the increase in lipid tail disorder and the induction of local curvature on the lipid head-groups by the peptides. From all the simulations, we conclude that the hydrogen bonding interactions between the lysines of the peptides and the oxygens of the polar lipid head-groups are the strongest and determine the overall peptide binding characteristics to the lipids.

Antimicrobial Cationic Peptides↗

PubMed2003

Light-induced molecular cutting: localized reaction on a single DNA molecule.

A short focused pulse of light was used to selectively cut lambda-phage DNA molecules at specific restriction sites. Lambda DNA (48.5 kbp) was stretched and placed in a solution containing a restriction enzyme (Sma 1), caged magnesium ions (using a DM-Nitrophen complex), and a chelating agent (EDTA). When a pulse of UV light was directed at a particular location on the stretched DNA molecule, magnesium ions were released into solution. A series of binding reactions then occur in which the enzyme and the chelating agent compete for free Mg2+ ions. Since Sma 1 functions only in the presence of Mg2+, as is true of most endonucleases, the site(s) in the vicinity of the pulse (typically approximately 6 microm) were cut while other sites (three total for this DNA/enzyme pair) were not. The ratio of the concentration of the chelating agent to that of the magnesium ions was used to control the radius of this reaction zone with higher ratios leading to smaller, localized reaction areas. This optically based reaction mechanism could be useful to understand single molecule enzymatic kinetics, and when coupled with other DNA analysis techniques, this could be used to construct complex genotyping and sequencing devices that would analyze parts of single DNA molecules.

Bacteriophage lambda↗

PubMed2003

Molecular engineering of peptides.

Deeper understanding of the role of short peptides in lipid layers has revealed potential applications for rationally designed synthetic replacements. A recent report illustrates the successful design of a peptoid mimic of SP-C, a protein linked to respiratory distress syndrome.

Drug Design↗

PubMed2002

Specific mode of interaction between components of model pulmonary surfactants using computer simulations.

Atomistic molecular dynamics simulations and structural bioinformatics tools enable the identification of the exact mode of interaction between model pulmonary surfactant components. Two nanosecond long simulations of the N-terminal region of human surfactant protein-B (SP-B(1-25)) in dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylglycerol (DPPG) monolayers of different lipid surface densities reveal the preferential affinity of SP-B(1-25) for anionic phospholipids. In particular, arginine 12 and lysine 24 interact strongly and with high specificity with the phosphate group of the DPPG lipids, stabilizing the position, the orientation, and the secondary structure of the peptide in the monolayer. The peptide lies at an oblique angle to the interfacial plane, ranging between 47 degrees and 62 degrees, increasing with decreasing lipid surface density. In DPPC monolayers the interaction is largely determined by hydrophobic interactions. The non-specific nature of DPPC-SP-B(1-25) interactions allows for significant flexibility in the topology of the peptide in the lipid matrix. Bioinformatics tools are employed to generalize the simulation results to the sequences of SP-B(1-25) in other organisms. The importance of specific residues, and the role of the largely helical and amphiphilic nature of the peptide in the functionality of SP-B(1-25) are established. The synergy of classical mechanics tools with bioinformatics methods greatly enhances the molecular-level interpretation of pulmonary surfactant action and facilitates the development of design rules for synthetic surfactant analogues.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2002

Electrostretching DNA molecules using polymer-enhanced media within microfabricated devices.

In this paper, we demonstrate immobilization and stretching of single lambda-phage DNA molecules within microfluidic systems using ac fields. We present a novel "thiol-on-gold"-based immobilization technique for fixing one specific end (3' end) of a DNA molecule onto a gold electrode. A polymer-enhanced medium (approximately 3.75 wt % linear polyacrylamide in Tris-HCl) is used to obtain fully stretched configurations (21 microm) of fluorescently stained lambda-DNA molecules. We also present an optimized microelectrode design with pointed electrodes and an electrode spacing of 20 microm for stretching DNA molecules with an ac field (1 MHz, 3 x 10(5) V/m). Finally, using these techniques, we immobilize a single DNA molecule at one electrode edge, stretch the molecule, and fix the other end at an adjacent electrode edge, forming a bridge between two electrodes within a microfabricated device.

Acrylic Resins↗

PubMed2002

Simulations of zwitterionic and anionic phospholipid monolayers.

Results of atomistic molecular dynamics simulations of dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylglycerol monolayers at the air/water interface are presented. Dipalmitoylphosphatidylcholine is zwitterionic and dipalmitoylphosphatidylglycerol is anionic at physiological pH. NaCl and CaCl2 water subphases are simulated. The simulations are carried out at different surface densities, and a simulation cell geometry is chosen that greatly facilitates the investigation of phospholipid monolayer properties. Ensemble average monolayer properties calculated from simulation are in agreement with experimental measurements. The dependence of the properties of the monolayers on the surface density, the type of the headgroup, and the ionic environment are explained in terms of atomistically detailed pair distribution functions and electron density profiles, demonstrating the strength of simulations in investigating complex, multicomponent systems of biological importance.

1,2-Dipalmitoylphosphatidylcholine↗