Binding molecules

Fogel, M., and Hastings, J. W. (1971). A substrate binding molecule in the Gonyaulax bioluminescence reaction. Arch. Biochem. Biophys. 142 310-321. 

The availability of sequence-specific DNA binding molecules led to the development of bifunctional polyamides that covalently react with the minor groove of DNA. Two classes of alkylating agents were conjugated to the hairpin turn unit and bound proximal to their alkylation sites by a DNA-binding polyamide [58, 59]. 

Dervan, P. B. Design oe sequence-specific DNA-binding molecules. Science 1986, 232, 464-471. 

The initial hurdle to overcome in the biosensor application of a nucleic acid is that involving its stable attachment on a transducing element which commonly includes a metallic electrode. In the first part of this chapter, we wish to introduce our approach for DNA immobilization (Scheme 1). A detailed characterization of the immobilization chemistry is also presented. In the second part, we follow the development of work from our laboratory on chemical sensor applications of the DNA-modified electrode involving a biosensor for DNA-binding molecules and an electrochemical gene sensor. 

In the first section of the Review, the basic neurobiology of PCP was emphasized. Studies on the binding of PCP to specific receptor molecules in brain have been confounded by the presence of two types of PCP-binding molecules. GUNDLACH reported that he was able to distinguish a PCP-binding site from an opiate-binding site that also binds PCP. The two sites had different localizations in brain and produced different behaviors. ZUKIN also separated the two receptors and reported on the early development of the PCP receptor in brain. He described the isolation from brain of a substance that reacts specifically with the PCP receptor. 

For a soluble enzyme that is not part of a multi-enzyme complex, the fastest rate of enzyme-inhibitor association is determined by the rate of molecular collisions between the two binding partners (i.e., the enzyme and the inhibitor) in solution. The rate of molecular collisions is in turn controlled by the rate of diffusion. The diffusion-limited rate of molecular collisions is dependent on the radii of the two binding molecules and the solution temperature and viscosity (Fersht, 1999) ... 

Microbes that lack a specific active transport system for removing toxic metals may be able to sequester heavy metals either inside or outside of the cell. Intracellular sequestration occurs when cytoplasmic metal-binding molecules are produced in response to metal stress, preventing the metals from interacting with vital cell structures. The two most common molecules used for intracellular... 

Adsorption enthalpies and vibrational frequencies of small molecules adsorbed on cation sites in zeolites are often related to acidity (either Bronsted or Lewis acidity of H+ and alkali metal cations, respectively) of particular sites. It is now well accepted that the local environment of the cation (the way it is coordinated with the framework oxygen atoms) affects both, vibrational dynamics and adsorption enthalpies of adsorbed molecules. Only recently it has been demonstrated that in addition to the interaction of one end of the molecule with the cation (effect from the bottom) also the interaction of the other end of the molecule with a second cation or with the zeolite framework (effect from the top) has a substantial effect on vibrational frequencies of the adsorbed molecule [1,2]. The effect from bottom mainly reflects the coordination of the metal cation with the framework - the tighter is the cation-framework coordination the lower is the ability of that cation to bind molecules and the smaller is the effect on the vibrational frequencies of adsorbed molecules. This effect is most prominent for Li+ cations [3-6], In this contribution we focus on the discussion of the effect from top. The interaction of acetonitrile (AN) and carbon monoxide with sodium exchanged zeolites Na-A (Si/AM) andNa-FER (Si/Al= 8.5 and 27) is investigated. 

Another crosslinker, SAED (Chapter 5, Section 3.9), can be used in a similar fashion, but instead of transferring a radioactive label, it contains a fluorescent portion that is transferred to a binding molecule after cleavage. Similarly, sulfo-SBED routinely is used to study protein interaction. Cleavage of a disulfide bridge after capture of interacting proteins results in transfer of a biotin label to the unknown prey protein (Chapter 28, Section 3.1). The biotin modification then can be used to detect or isolate the unknown interactor for subsequent identification. 

The effect of the amino acid spacer on iron(III) affinity was investigated using a series of enterobactin-mimic TRENCAM-based siderophores (82). While TRENCAM (17) has structural similarities to enterobactin, in that it is a tripodal tris-catechol iron-binding molecule, the addition of amino acid spacers to the TRENCAM frame (Fig. 10) increases the stability of the iron(III) complexes of the analogs in the order ofbAla (19)complex stability is attributed to the intramolecular interactions of the additional amino acid side chains that stabilize the iron-siderophore complex slightly. 

The generation of trimethylenemethane diyls [26] has been shown to effect DNA cleavage. Attachment of this group to a DNA binding molecule (Fig. 7) made the intramolecular hydrogen atom abstraction (DNA-drug being considered as one molecule) more efficient than the competitive dimerization of diyls. 

Significant progress has been achieved in the preceding few years in the study of titanosilicate molecular sieves, especially TS-1, TS-2, Ti-beta, and Ti-MCM-41. In the dehydrated, pristine state most of the Ti4+ ions on the surfaces of these materials are tetrahedrally coordinated, being present in either one of two structures a tetrapodal (Ti(OSi)4) or a tripodal (Ti(OSi)3OH) structure. The former predominates in TS-1, TS-2, and Ti-beta, and the latter is prominent in Ti-MCM-41. The Ti ions are coordinatively unsaturated and act as Lewis acid sites that coordinatively bind molecules such as H20, NH3, CH3CN, and H202. Upon interaction with H202 or H2 + 02, the Ti ions form titanium oxo species. Spectroscopic techniques have been used to identify side-bound hydroperoxo species such as Ti(02H) and superoxo structures such as Ti(02 ) on these catalysts. 

At the EM level, detection usually involves using a probe (oligonucleotide) in which a hapten has been incorporated. Incorporation of the hapten does not interfere with the hybridization of the complementary sequences. The next step is the binding of a reporter (may be an antibody) to the hapten. The reporter is then subjected to a binding molecule (may be a secondary antibody) that is coupled with an electron-dense material such as colloidal gold for visualization. Nonetheless, the many affinity-detection and immunodetection systems developed for immuno-cytochemistry may now with ingenuity be applied to molecular biology at the EM level. 

Olfaction, once thought to be a primitive sense, is now recognized as an elaborate sensory system that deploys a large family of odorant receptors to analyse the chemical environment. Interactions between these receptors and their diverse natural binding molecules (ligands) translate the world of odors into a neural code. Humans have about 350 odorant receptors. Rodents have more than a thousand. 

Determination of the thermodynamic and kinetic parameters of interest requires monitoring of the surface concentration of the binding molecule. With large biomolecules, the surface concentrations are small, and simple redox labeling will not allow sufficient sensitivity. Labeling of the target biomolecule with a redox enzyme obviates this difficulty, thanks to the catalytic properties of the enzyme. 

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