Biomedical subjects

B A Stillman

Publications and source records attributed to B A Stillman.

4 recordsLinked to original sources

PubMed2001

Expression microarray hybridization kinetics depend on length of the immobilized DNA but are independent of immobilization substrate.

Expression microarrays are often constructed by the immobilization of PCR products on two-dimensional modified glass slides or on three-dimensional microporous substrates. In this study we investigate whether the length of the immobilized species and the substrate choice influence hybridization dynamics. Using a simple bimolecular mass action controlled model to describe hybridization, we observed that the extent of hybridization and the initial velocities were directly dependent on the length of the immobilized species. An inflection point was noted at a length of 712 bases, above which the influence of length on hybridization rate decreased. Interestingly, we observed no differences in these parameters whether hybridization occurred on a two- or three-dimensional surface. Furthermore, the affinity of the solution phase labeled species for the immobilized species was identical for all arrayed lengths on both surfaces. These data indicate a similar interaction of the noncovalently immobilized species with either surface. Finally, we have determined that competitive hybridization on expression microarrays is nonlinear with respect to time and concentration of competitor. This observation is critical for analysis of expression array data.

Base Pairing↗

PubMed2000

FAST slides: a novel surface for microarrays.

We have evaluated FAST slides, a glass slide with a microporous polymeric surface that is a suitable substrate for microarray technology. The surface is a nitrocellulose-based polymer that binds DNA and proteins in a noncovalent but irreversible manner. FAST slides are compatible with robotic systems currently used to create microarrays and can easily accommodate volumes of 0.03-2 nL/spot. Our data indicate that FAST slides have a much higher binding capacity for DNA and better spot-to-spot consistency than traditional poly-lysine-coated slides. In addition, FAST slides are well suited for fluorescent detection because of their relatively low light scatter and efficient retention of arrayed DNA. These properties translate into fluorescent sensitivity comparable to modified glass surfaces. FAST slides are also ideal for arraying proteins, making them the only substrate of their kind currently available for microarray applications.

Biotinylation↗

PubMed1999

Importance of the extracellular domain for prostaglandin EP(2) receptor function.

The ligand binding pocket of biogenic amine G protein-coupled receptors is embedded in the membrane-spanning regions of these receptors, whereas the extracellular domains of the peptidergic receptors play a key role in the structure and function of this class of receptors. To examine the role of the extracellular sequences in prostaglandin receptor-ligand interaction, chimeras were constructed with the two G(s)-coupled E-prostanoid (EP) receptors, replacing each of the extracellular sequences of the human EP(2) receptor with the corresponding human EP(4) receptor residues. Replacement of the third extracellular loop (ECIII) yielded a receptor that binds [(3)H]prostaglandin E(2) (PGE(2); K(d) = 6.3 nM) with similar affinity as the EP(2) wild-type receptor (K(d) = 12.9 nM). Similarly, replacement of the nonconserved carboxyl-terminal portion of ECII resulted in a receptor that maintains [(3)H]PGE(2) binding (K(d) = 8.8 nM). In contrast, replacement of the amino terminus, ECI, the entire ECII region, or the residues within the highly conserved motif of the amino-terminal half of ECII yielded chimeras that displayed neither detectable [(3)H]PGE(2) binding nor receptor-evoked cAMP generation. Immunoprecipitation demonstrated that each chimera is expressed at levels near that of wild-type receptors; however, enzyme-linked immunosorbent assay revealed that inactive chimeras have reduced cell surface expression. Similarly, chimeras that exchange the multiple extracellular loop sequences N/ECI, ECII/ECIII, or all four sequences lacked detectable binding and signal transduction, and although expressed, were not detected on the cell surface. These data suggest that the extracellular sequences of the EP(2) receptor are critical determinants of receptor structure and/or function, unlike other G protein-coupled receptors that bind small molecules.

Amino Acid Sequence↗

PubMed1998

A conserved threonine in the second extracellular loop of the human EP2 and EP4 receptors is required for ligand binding.

G protein coupled receptors for prostaglandins are activated when agonists are bound to a binding pocket formed in part by the seven transmembrane domains. Recent studies have determined that substitution of a conserved threonine in the second extracellular loop of the prostaglandin EP3 receptor resulted in increased affinity for ligands with a C1 methyl ester moiety. The homologous threonine in the second extracellular loop of the human prostaglandin EP2 and EP4 receptors was mutated to alanine. When expressed in COS1 cells, detectable radioligand binding at both of these receptors bearing the threonine to alanine substitution (EP2T185A; EP4T168A) was abolished, as well as the receptors' ability to stimulate intracellular [cAMP]. In contrast, EP2 and EP4 receptors bearing conservative threonine to serine mutations (EP2T185S; EP4T168S) displayed Kd values for [3H]prostaglandin E2 similar to wild type receptors: 8.8 +/- 0.7 nM for EP2T185S compared to 12.9 +/- 1.2 nM for EP2 wild type; 2.0 +/- 0.8 nM for EP4T168S compared to 0.9 +/- 0.3 nM for the EP4 wild type receptor. The EC50 values for cAMP stimulation were 1.3 +/- 0.6 nM for EP2 wild type; 2.7 +/- 1.3 nM for EP2T185S; 1.1 +/- 0.3 nM for EP4 wild type; and 1.4 +/- 0.33 nM for EP4T168S. These studies suggest a critical role for the hydroxyl moiety on these conserved threonine residues at position 168/185 of the second extracellular loop in prostaglandin receptor-ligand interactions.

Amino Acid Substitution↗