Intercalating probes

These observations were significant to our choice of reactants for probing CT at DNA-modified surfaces. In particular, an upright orientation of the DNA relative to the surface is required to probe DNA-mediated reactions otherwise a more direct reaction between an intercalating probe and the electrode might be possible. Consequently, reactants were selected such that a negative potential could be apphed, thereby initiating reduction of an intercalated redox probe distantly bound within DNA helix. Importantly, the... 

Kohler O, Jarikote DV, Seitz O. Forced Intercalation Probes (FIT Probes) Thiazole orange as a fluorescent base in peptide nucleic 39. acids for homogeneous single-nucleotide-polymorphism detection. ChemBioChem. 2005 6 69-77. 

While many fundamental questions remain regarding the mechanism of electron transfer through the films, it is empirically clear that the characteristic electrochemical responses of intercalating probe molecules can signal even subtle perturbations within the double helix. The possibility that similar DNA-mediated electrochemical reactions might play important roles within the cell - for example, in the cathodic protection of... 

Methods to study the biosynthesis of RNA in living cells, their intracellular transport, subcellular localization, and degradation are of great interest for understanding cellular networks and their malfunction [1-3] during diseases. Here, we describe the live cell RNA imaging with peptide nucleic acid-based FIT forced intercalation probes that enabled a simultaneous localization of two viral messenger ribonucleic acid (mRNA) molecules. 

Boc- and Fmoc-terminated fluorescent fluorescein PNA monomer units were synthesized by means of solid-phase synthesis, and the products had photophysical properties comparable to nonmodifled fluorescein conjugates. 2-Aminopurine (2-ap) was the first fluorophore incorporated into a PNA strand for the purpose of examining PNA-DNA complexation via fluctuation in fluorescence emission. A more sophisticated sensing design was introduced by Seitz et al. that utilized the intercalator dye thiazole orange, termed a forced intercalation probe (FIT probe), for the determination of base pair mismatches within a duplex. ... 

The first smdies of redox reactions occurring within films composed of DNA duplexes were first conducted with methylene blue (MB) [23], an intercalating probe that exhibits a low-energy, reversible reduction at -0.25 V vs. SCE. Pronounced electrochemical signals exhibiting the features expected for a surface-bound species were observed at low intercalator concentrations, indicating that MB bound with high affinity to the modified electrode surface. Quantitation of the... 

The detection of a base mismatch by the intercalating probe DM was not highly sensitive to the position of the mismatch within the film or to the composition of the DNA duplex composing the film [25]. Sequences featuring mismatches at different locations and mismatched within different sequence contexts were evaluated accurate discrimination of fully paired versus mismatched sequences was achieved in all cases, although the incorporation of the mismatch at a position deep within the interior of the monolayer yielded the highest TA/CA current ratios. 

Attempts to elucidate the bonding have concentrated mainly on graphite-FeCla- This intercalate is especially suitable as a model compound, because the magnetic and Mossbauer properties of the iron nucleus constitute excellent probes for electronic structure and environment of the latter. 

CTC, used extensively to monitor calcium release in both whole cells and isolated organelles (28-33), is an amphipathic molecule that easily passes through cell membranes (see Figure 1). The fluorescence of this probe is enhanced more than fiftyfold by binding of calcium when the dye is intercalated into biological membranes. 

The nano-scale structures in polymer layered-silicate nano-composites can be thoroughly characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM). XRD is used to identify intercalated structures. XRD allows quantification of changes in layer spacing and the most commonly used to probe the nano-composite structure and... 

Metallointercalators, Organic Intercalators and Modified Bases as Probes... 

Redox participants are chosen to facilitate spectroscopic, biochemical and electrochemical probing of DNA CT. These include metallointercalators, organic intercalators, and modified bases that possess useful, well-described, and varied redox, photophysical and photochemical properties (Table 1). Our probes are readily incorporated into DNA assemblies where CT distances ranging from 3.4 to 200 A and driving forces spanning over two volts can be modulated with certainty. Most importantly, all redox probes which afford fast and/or efficient CT through DNA are well-coupled to the 7r-stack. 

The first experiments characterizing DNA-mediated CT over a precisely defined distance between covalently appended redox probes were reported in 1993 [95]. Remarkably, the luminescence of a photoexcited Ru(II) intercala-tor was quenched by a Rh(III) intercalator fixed to the other end of a 15-mer DNA duplex over 40 A away (Fig. 4). Furthermore, non-intercalating, tethered Ru(II) and Rh(III) complexes did not undergo this quenching reaction. In this way the importance of intercalative stacking for efficient CT was demonstrated. 

In order to directly probe the dynamics of CT between Et and ZG, and to understand how the intervening DNA base stack regulates CT rate constants and efficiencies, we examined this reaction on the femtosecond time scale [96]. These investigations revealed not only the unique ability of the DNA n-stack to mediate CT, but also the remarkable capacity of dynamical motions to modulate CT efficiency. Ultrafast CT between tethered, intercalated Et and ZG was observed with two time constants, 5 and 75 ps, both of which were essentially independent of distance over the 10-17 A examined. Significantly, both time constants correspond to CT reactions, as these fast decay components were not detected in analogous duplexes where the ZG was re-... 

Acridine and its derivatives are also fused nitrogen heterocycles similar to acridones, which display a high fluorescence quantum yield and possess the ability to intercalate tightly, though reversively, to the DNA helical structure [73], with large binding constants [74]. As a result, acridine dyes are recognized in the field of the development of probes for nucleic acid structure and conformational determination [75-77]. 

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