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Biomedical subjects

Kevin Burgess

Publications and source records attributed to Kevin Burgess.

At least 19 recordsLinked to original sources
PubMed2006

Syntheses, photophysical properties, and application of through-bond energy-transfer cassettes for biotechnology.

We have designed fluorescent "through-bond energy-transfer cassettes" that can harvest energy of a relatively short wavelength (e.g., 490 nm), and emit it at appreciably longer wavelengths without significant loss of intensity. Probes of this type could be particularly useful in biotechnology for multiplexing experiments in which several different outputs are to be observed from a single excitation source. Cassettes 1-4 were designed, prepared, and studied as model systems to achieve this end. They were synthesized through convergent routes that feature coupling of specially prepared fluorescein- and rhodamine-derived fragments. The four cassettes were shown to emit strongly, with highly efficient energy transfer. Their emission maxima cover a broad range of wavelengths (broader than the four dye cassettes currently used for most high-throughput DNA sequencing), and they exhibit faster energy-transfer rates than a similar through-space energy-transfer cassette. Specifically, energy-transfer rates in these cassettes is around 6-7 ps, in contrast to a similar through-space energy-transfer system shown to have a decay time of around 35 ps. Moreover, the cassettes are considerably more stable to photobleaching than fluorescein, even though they each contain fluorescein-derived donors. This was confirmed by bulk fluorescent measurements, and in single-molecule-detection studies. Modification of a commercial automated DNA-sequencing apparatus to detect the emissions of these four energy-transfer cassettes enabled single-color dye-primer sequencing.

Biotechnology↗
PubMed2006

Syntheses and properties of water-soluble Nile Red derivatives.

Nile Red (compound A) fluoresces at about 530 nm with good quantum yields in apolar solvents. In more polar ones its fluorescence emission shows a dramatic, and potentially useful, shift to about 640 nm, but its quantum yield is significantly reduced. Further, Nile Red has a very poor solubility in aqueous media. The hypothesis tested in this paper is that Nile Red derivatives that incorporate water-solubilizing groups will tend to fluoresce with good quantum yields in aqueous media, and in the more useful wavelength range around 640 nm. Thus three Nile Red derivatives, 1-3, were prepared. Compound 1 had three hydroxyl groups more than Nile Red, but was surprisingly insoluble in aqueous media. However, the dicarboxylic acid 2 and carboxylic/sulfonic acid derivative 3 showed excellent water solubilities. Spectral data for 2 and 3 showed that they do indeed fluoresce with good quantum yields in the 640 nm region in aqueous media. These properties of compounds 2 and 3 might be useful in the development of fluorescent probes for biotechnology.

Fluorescence↗
PubMed2006

Water-soluble through-bond energy transfer cassettes for intracellular imaging.

A special, water-soluble, fluorescent probe 1 was designed. This consisted of a fluorescein-based component to harvest irradiation at 488 nm and a rhodamine-based part designed to emit it at a significantly longer wavelength. This cassette was used to label an illustrative protein called ACBP. Evidence was accumulated to support the assertion that ACBP-1 bound its native ligand with a binding constant similar to that of the unlabeled protein, and retained its secondary structure (CD). ACBP-1 was imported into cells using the Chariot peptide. Confocal images proved that some ACBP-1 localized into the nucleus (as expected) and, most significantly, it could be visualized more effectively by irradiating at the donor (fluorescein-like) part of the cassette, than the acceptor (rhodamine-like) part. Overall, this study demonstrates that cassettes of this kind can label a protein without significantly perturbing its function or secondary structure and they can be visualized effectively via irradiation of the donor and observation of the acceptor fluorescence.

Energy Transfer↗
PubMed2006

Cyclic semipeptoids: peptoid-organic hybrid macrocycles.

[structure: see text] Cyclic semipeptoids 1 and 2 represent constrained, secondary structure mimics where the R(1) and R(2) side chains correspond to those of amino acids. Solid-phase syntheses and conformational analyses of these compounds are described.

Amino Acids↗
PubMed2006

Heterovalent selectivity and the combinatorial advantage.

Libraries of monovalent compounds can be reacted with each other to give libraries of bivalent ones. If those reactions are efficient, and if the products do not need to be purified, large numbers of bivalent compounds can be produced rapidly, and one might say there is a "combinatorial advantage" to doing so. However, selective formation of heterobivalent products must be possible otherwise statistical mixtures will form. This tutorial review describes methods that will give heterobivalent compounds almost exclusively. Although there are relatively few methods that will give that desired selectivity, such methods are becoming increasingly important as the potential applications of bi- and multivalent compounds emerge.

Journal Article↗
PubMed2005

Mechanistic insights into iridium-catalyzed asymmetric hydrogenation of dienes.

Hydrogenation of 2,3-diphenylbutadiene (1) with the chiral carbene-oxazoline-iridium complex C has been studied by means of a combined experimental and computational approach. A detailed kinetic profile of the reaction was obtained with respect to consumption of the substrate and formation of the intermediate half-reduction products, 2,3-diphenylbut-1-ene (2) and the final product, 2,3-diphenylbutane (3). The data generated from these analyses, and from NMR experiments, revealed several facets of the reaction. After a brief induction period (presumably involving reduction of the cyclooctadiene ligand on C), the diene concentration declines in a zero-order process primarily to give monoene intermediates. When all the diene is consumed, the reaction accelerates and compound 3 begins to accumulate. Interestingly, the prevalent enantiomer of the monoene intermediate 2 is converted mostly to meso-3 so the enantioselectivity of the reaction appears to reverse. The reaction seems to be first-order with respect to the catalyst when the catalyst concentration is less than 0.0075 M; diffusion of hydrogen across the gas-liquid interface complicates the analysis at higher catalyst concentrations. Similarly, these diffusion effects complicated measurements of reaction rate versus applied pressure of dihydrogen; other factors like stir speed and flask geometry come into play under some, but not all, the conditions examined. Density functional theory (DFT) calculations, using the PBE method, were used to probe the reaction. These studies indicate a transoid-eta(4)-diene-dihydride complex forms in the first stages of the catalytic cycle. Further reaction requires dissociation of one alkene ligand to give a eta(2)-diene-dihydride-dihydrogen intermediate. A catalytic cycle that features Ir(3+)/Ir(5+) seems to be involved thereafter.

Journal Article↗
PubMed2005

Ring closure to beta-turn mimics via copper-catalyzed azide/alkyne cycloadditions.

[Structure: see text]. Copper-catalyzed azide alkyne cycloadditions of the linear substrates 1 were used to form the cyclic derivatives 2. Computational, NMR, and CD analyses of these compounds indicate that their most favorable conformational states include type I and type II beta-turn conformations. Selectivity for the dimeric products 6 in these cyclization reactions is discussed.

Alkynes↗
PubMed2005

Selective small molecule peptidomimetic ligands of TrkC and TrkA receptors afford discrete or complete neurotrophic activities.

We designed a minilibrary of 55 small molecule peptidomimetics based on beta-turns of the neurotrophin growth factor polypeptides neurotrophin-3 (NT-3) and nerve growth factor (NGF). Direct binding, binding competition, and biological screens identified agonistic ligands of the ectodomain of the neurotrophin receptors TrkC and TrkA. Agonism is intrinsic to the peptidomimetic ligand (in the absence of neurotrophins), and/or can also be detected as potentiation of neurotrophin action. Remarkably, some peptidomimetics afford both neurotrophic activities of cell survival and neuronal differentiation, while others afford discrete signals leading to either survival or differentiation. The high rate of hits identified suggests that focused minilibraries may be desirable for developing bioactive ligands of cell surface receptors. Small, selective, proteolytically stable ligands with defined biological activity may have therapeutic potential.

Animals↗
PubMed2004

Electronic effects steer the mechanism of asymmetric hydrogenations of unfunctionalized aryl-substituted alkenes.

Density functional theory (PBE and B3LYP) was used to study asymmetric hydrogenations of alkenes catalyzed by an iridium imidazolylidine oxazoline complex. The calculation predicts that the alkene preferentially coordinates to the site trans to the carbene. The coordinated alkene then reacts first with the H2 ligand, then with the hydride to form alkane. Finally, the alkane is released by equilibrating with extrinsic H2 and alkene. Enantioface selectivities for hydrogenations of trisubstituted alkenes seem to be driven primarily by steric interactions with the adamantyl part of the ligand; only the smallest substituents can adopt a site close to it. Application of this theoretical model leads to correct predictions regarding the experimentally observed sense and magnitude of the enantioselectivities.

Journal Article↗
PubMed2004

Long-lasting rescue of age-associated deficits in cognition and the CNS cholinergic phenotype by a partial agonist peptidomimetic ligand of TrkA.

Previously, we developed a proteolytically stable small molecule peptidomimetic termed D3 as a selective ligand of the extracellular domain of the TrkA receptor for the NGF. Ex vivo D3 was defined as a selective, partial TrkA agonist. Here, the in vivo efficacy of D3 as a potential therapeutic for cholinergic neurons was tested in cognitively impaired aged rats, and we compared the consequence of partial TrkA activation (D3) versus full TrkA/p75 activation (NGF). We show that in vivo D3 binds to TrkA receptors and affords a significant and long-lived phenotypic rescue of the cholinergic phenotype both in the cortex and in the nucleus basalis. The cholinergic rescue was selective and correlates with a significant improvement of memory/learning in cognitively impaired aged rats. The effects of the synthetic ligand D3 and the natural ligand NGF were comparable. Small, proteolytically stable ligands with selective agonistic activity at a growth factor receptor may have therapeutic potential for neurodegenerative disorders.

Acetylcholine↗
PubMed2004

A blue-to-red energy-transfer thymidine analogue that functions in DNA.

The thymidine analogue 1 is a blue-to-red energy transfer cassette designed to absorb UV light in the 300 nm region and emit it as fluorescence at around 520 nm. When incorporated into DNA, the fluorescence intensity of this modified nucleobase is not significantly reduced by the surrounding structure in the oligonucleotides. [structure--see text]

Base Sequence↗