Aptamers as therapeutic and diagnostic reagents: problems and prospects.

Aptamers are nucleic acid molecules that bind specific ligands. Barriers to the application of aptamers as therapeutic and diagnostic reagents have been overcome in the past several years. In particular, aptamers that bind biomedically relevant targets have proven to be efficacious at modifying cellular metabolism. Such aptamers can be stabilized by chemical modifications and potentially used in vivo. Researchers have begun to devise aptamer-based diagnostic assays that may rival more conventional immunoassays.

Thermodynamic properties of a conformationally constrained intramolecular DNA triple helix.

We describe the thermodynamic properties of an intramolecular triple helix with two all-thymine linker loops in which the Hoogsteen strand is covalently crosslinked to the underlying Watson-Crick hairpin duplex by means of a disulfide bridge. We compare these properties to those of the corresponding intramolecular triplex without the disulfide crosslink. Optical and calorimetric measurements reveal that the uncrosslinked parent triplex melts in a biphasic manner above pH 6, with the initial triplex to duplex transition (Hoogsteen strand release) occurring at lower temperatures than subsequent melting of the hairpin helix. By contrast, crosslinking increases the thermal stability of the Hoogsteen transition such that the triplex and underlying hairpin duplex melt as a single transition under all conditions studied. Model independent thermodynamic data obtained by differential scanning calorimetry reveals the crosslink-induced increase in triplex thermal stability corresponds to a free energy stabilization of about 3 kcal/mol, with this stabilization being entirely entropic in origin. In other words, the crosslink is enthalpically neutral, but nevertheless, induces a triplex stabilization of 3 kcal/mol due to a reduction in the entropy change associated with triplex melting. In an effort to define the origin(s) of this entropic impact, we measured the pH and ionic strength dependence of the melting transitions. From a comparison of the melting transitions at different pH values and ionic strengths, we estimate that 0.4 more protons are associated with the crosslinked triplex state than with the uncrosslinked triplex, and 1.3 fewer counterions are released on melting the crosslinked triplex. We discuss how such crosslink-induced changes in proton binding and counterion release, in conjunction with potential changes in hydration and conformational freedom, could combine to give rise to the observed changes in entropy.

Binding determinants of the sialic acid-specific lectin from the slug Limax flavus.

The specific structural features of 24 N-acetylneuraminic acid derivatives required for the high affinity interaction of sialoglycoconjugates with the sialic acid-specific lectin from the slug Limax flavus were studied by hapten inhibition of precipitation. These results provide insight regarding the structure of the binding pocket for N-acetylneuraminic acid that exists in L. flavus agglutinin (LFA). The alpha-anomer of sialic acid is a very important factor in binding to the slug lectin. The carboxylic acid group makes only a moderate contribution to binding, since modifications of the carboxylic group decrease binding approximately 5-fold. Modification or removal of the hydroxyl group on carbon 4 does not affect binding. However, when the C4 epimer was tested, there was a dramatic decrease in binding, suggesting that whereas the equatorial hydroxyl at C4 does not contribute to binding, the introduction of an axial hydroxyl group at C4 sterically hinders the binding interaction. The substituent on the 5-amino group occupies an important role in binding of Neu5Ac to LFA as well. When the acetyl is modified by the addition of a hydroxyl group to yield the N-glycolyl derivative, we observed a 20-fold decrease, while the removal of the methyl to form the N-formyl derivative resulted in a 50-fold decrease. The 5-amino derivative was the poorest inhibitor of all compounds examined, indicating a critical role for the N-acetyl group in high affinity binding to LFA. The glyceryl tail also appears to be critical for binding inasmuch as acetylation of the C9 hydroxyl group or periodate cleavage of carbons 8 and 9 resulted in a 20- to 50-fold decrease in binding. The equilibrium constant (K(a)) for binding of Neu5Ac to LFA is 3.8 x 10(4) M-1, with a single binding site (n = 0.85) per monomer.

Conformational studies of hairpin sequences from the ColE1 cruciform.

Inverted repeat sequences derived from the ColE1 cruciform were investigated by nuclear magnetic resonance (NMR) and UV spectroscopy. It was shown that 15 different sequences exist as stable hairpin structures over a range of buffer conditions and DNA concentrations. Experiments with six oligomers (1-6) containing the native stem sequence and five base loops, found that the two hairpins with the wild-type loops (1-2) served as upper and lower bounds for the thermodynamic stability of all the other sequences. NMR experiments, including rotational correlation time measurements and NOESY spectra, were then performed on 1, the most stable hairpin sequence to begin to uncover a structural basis of its stability.

Synthesis of high-affinity, hydrophobic monosaccharide derivatives and study of their interaction with concanavalin A, the pea, the lentil, and fava bean lectins.

Concanavalin A (Con A) and agglutinins from the pea (PSA), lentil (LCH), and fava bean (VFA) constitute a group of D-mannose/D-glucose binding legume lectins. In addition to their sugar binding specificity, these lectins also contain sites that bind hydrophobic ligands. The present study explores a class of nonpolar binding sites reportedly present adjacent to the carbohydrate binding site in PSA, LCH, and VFA. A series of 2-O- and 3-O-substituted nitrobenzoyl and nitrobenzyl derivatives of methyl alpha-D-glucopyranoside and methyl alpha-D-mannopyranoside were synthesized. Evaluation of their binding to Con A, PSA, LCH, and VFA was carried out by the technique of hapten inhibition of precipitation reaction. The hapten inhibition assay results reveal that the presence of a methyl or methylene group at the O-2 or O-3 position of the sugar is essential for hydrophobic interaction with PSA, LCH, and VFA. The substitution of methyl by nitrobenzyl leads to enhanced binding (1.7-16.7 times for the 2-O-substituted compounds and 7.9-40.5 times for the 3-O-substituted compounds) with the m-nitrobenzyl group contributing to maximum binding. A hydrophobic interaction is also involved between Con A and 2-O-nitrobenzyl derivatives, resulting in enhanced binding, but the corresponding 3-O-isomers bind poorly due probably to steric reasons. These results may be rationalized on the basis of the recently published X-ray data of Con A and VFA. The nitrobenzyl derivatives, after transformation to their azido analogs, have potential applications in the photoaffinity labeling of these lectins.

Phosphate/calcium alterations in the first stages of Alzheimer's disease: implications for etiology and pathogenesis.

The present study tested aspects of a novel etiological/pathogenetic hypothesis of Alzheimer's disease (AD), which proposes that alterations in endocrine regulation of peripheral calcium/phosphate (Ca/PO4) homeostasis (e.g., by glucocorticoids, vitamin D, etc.) induce and/or reflect altered calcium homeostasis and neurotoxicity in brain neurons. Two key predictions of this hypothesis were tested, namely that: (1) alterations in serum Ca and/or PO4 regulation should be present before or near the onset of AD and (2) these alterations should be found consistently in subjects with unconfounded AD. Previous studies have sought evidence of changes in Ca regulation primarily late in the disease, and usually in severely demented, thin and immobile inpatients in whom Ca/PO4 measures are likely to be confounded. In the present study, only mobile, relatively healthy, adequately nourished outpatients with probable AD were selected. In comparison to age-matched controls or demented subjects with even mild indications of vascular contributions, the AD subjects were characterized by lower serum PO4 and, to a lesser degree, lower serum Ca as well as a higher chloride/PO4 ratio. On serum chemistry tests from the first stages of AD (within 1 or 3 years after the onset of cognitive symptoms), these changes in serum PO4/Ca were as pronounced as they were later in the disease. Moderately low values of either PO4, Ca, or both (below -1.0 S.D. from the control group mean) identified 74% of all AD subjects and 100% of early onset AD subjects, in comparison to only 46% of mixed/vascular dementia subjects and 31% of normal age-matched controls. Thus, the results were consistent with the predictions and may have significant etiological/pathogenetic implications. If larger tests confirm these frequencies, serum Ca/PO4 indices may also prove useful in differential diagnosis.