DNA meter: Energy tunable, quantitative hybridization assay.

We describe a novel hybridization assay that employs a unique class of energy tunable, bulge loop-containing competitor strands (C*) that hybridize to a probe strand (P). Such initial "pre-binding" of a probe strand modulates its effective "availability" for hybridizing to a target site (T). More generally, the assay described here is based on competitive binding equilibria for a common probe strand (P) between such tunable competitor strands (C*) and a target strand (T). We demonstrate that loop variable, energy tunable families of C*P complexes exhibit enhanced discrimination between targets and mismatched targets, thereby reducing false positives/negatives. We refer to a C*P complex between a C* competitor single strand and the probe strand as a "tuning fork," since the C* strand exhibits branch points (forks) at the duplex-bulge interfaces within the complex. By varying the loop to create families of such "tuning forks," one can construct C*P "energy ladders" capable of resolving small differences within the target that may be of biological/functional consequence. The methodology further allows quantification of target strand concentrations, a determination heretofore not readily available by conventional hybridization assays. The dual ability of this tunable assay to discriminate and quantitate targets provides the basis for developing a technology we refer to as a "DNA Meter." Here we present data that establish proof-of-principle for an in solution version of such a DNA Meter. We envision future applications of this tunable assay that incorporate surface bound/spatially resolved DNA arrays to yield enhanced discrimination and sensitivity.

Nanogap dielectric spectroscopy for aptamer-based protein detection.

Among the various label-free methods for monitoring biomolecular interactions, capacitive sensors stand out due to their simple instrumentation and compatibility with multiplex formats. However, electrode polarization due to ion gradient formation and noise from solution conductance limited early dielectric spectroscopic measurements to high frequencies only, which in turn limited their sensitivity to biomolecular interactions, as the applied excitation signals were too fast for the charged macromolecules to respond. To minimize electrode polarization effects, capacitive sensors with 20 nm electrode separation were fabricated using silicon dioxide sacrificial layer techniques. The nanoscale separation of the capacitive electrodes in the sensor results in an enhanced overlapping of electrical double layers, and apparently a more ordered "ice-like" water structure. Such effects in turn reduce low frequency contributions from bulk sample resistance and from electrode polarization, and thus markedly enhance sensitivity toward biomolecular interactions. Using these nanogap capacitive sensors, highly sensitive, label-free aptamer-based detection of protein molecules is achieved.

Toxin binding of tolevamer, a polyanionic drug that protects against antibiotic-associated diarrhea.

Tolevamer, (GT160-246), is a sodium salt of styrene sulfonate polymer that is under development for the treatment of diarrhea caused by infection with Clostridium difficile. Pulsed ultrafiltration binding experiments in phosphate buffer containing 0.15 M Na(+) provide per polymer chain dissociation constants of 133 nM and 8.7 microM for the binding of tolevamer to C. difficile toxins A and B, respectively. At 0.05 M Na(+), the binding of toxin A to tolevamer is irreversible, whereas the dissociation constant to toxin B under these conditions is 120 nM. Binding constants obtained from fluorescence polarization data for toxin A binding to tolevamer at 0.15 M Na(+) agree substantially with those obtained by pulsed ultrafiltration. The binding activity of tolevamer reported here correlates well with previously reported results for the inhibition of the biological activity of C. difficile toxins A and B. From the fluorescence polarization data, it is estimated that one toxin A molecule interacts with between 600 to 1000 monomer units on tolevamer at 0.15 M Na(+). Thus, the data suggest a very large interaction surface between polymer and toxin A.

Conformational screening of oligonucleotides by variable-temperature high performance liquid chromatography: dissecting the duplex-hairpin-coil equilibria of d(CGCGAATTCGCG).

This study probes the potential of variable-temperature high performance liquid chromatography (VT-HPLC) as a tool for dissecting and modulating nucleic acid structural transitions, using as a model the duplex-hairpin-coil transitions of d(CGCGAATTCGCG). It is demonstrated that VT-HPLC, combined with diode-array detection of the uv signal, enables, for the first time, a physical separation of spectroscopically distinct species that can be assigned to the duplex, hairpin, and coil forms of d(CGCGAATTCGCG). Although the species are spectroscopically distinguishable, they are not readily isolated. Hence, if fractions from the peaks for hairpin or duplex forms are collected and subsequently reinjected onto the cartridge, reequilibration occurs, and both hairpin and duplex peaks are observed. Area integration of the peaks corresponding to duplex and hairpin species provides a means to monitor the duplex to hairpin transition at effective concentrations in the nanomolar range, well below that accessible by conventional spectrophotometers. Concentration-dependent equilibrium constants, melting temperatures, and standard state enthalpies extracted from our measurements compare very well with previous literature results, and with our own results that take into account the effect of our solvent conditions [100 mM TEAA (triethylammonium acetate) and variable acetonitrile] on the melting behavior. By combining precise temperature control with separation based on size, physical behavior, and interaction free energies, VT-HPLC provides a powerful tool for both the modulation and the separation of nucleic acid conformations.

Bile acid binding to sevelamer HCl.

BACKGROUND: Clinical studies have shown sevelamer HCl (Renagel) to be effective for the reduction of serum phosphate in hemodialysis patients. These studies also consistently have demonstrated a significant reduction of low-density lipoprotein (LDL) cholesterol following treatment with sevelamer. METHODS: Equilibrium binding of bile acids and oleic acid was determined by incubating sevelamer with ligand containing buffer. Aliquots of the solution were filtered and the free ligand concentrations quantitated by high-pressure liquid chromatography (HPLC). Flow kinetics were determined using a cylindrical flow cell containing trapped sevelamer. Bile acid and oleic acid were pumped through the stirred cell in a manner designed to mimic the in vivo situation. Binding was monitored by HPLC. RESULTS: Sevelamer binds bile acids cooperatively and with high capacity. At low binding densities, the presence of the more hydrophobic bile acids enhances the binding of the less hydrophobic bile acids, and the presence of oleic acid enhances the binding of all bile acids. At saturating oleic acid concentrations, the bile acid binding capacity of sevelamer is reduced by only a factor of two. Moreover, the presence of oleic acid dramatically diminishes the release rate of bile acids from sevelamer. CONCLUSIONS: The favorable bile acid binding characteristics of sevelamer provide a compelling explanation for its ability to lower LDL cholesterol in hemodialysis patients and in healthy volunteers.