A proflavin molecule

In addition to the intercalated proflavine, there is a proflavine molecule that is sandwiched by adjacent, CpA dimer duplexes. The intercalated proflavine stacks more extensively with the C-C pair than with the A-A pair. The sandwiched proflavine stacks extensively with both the A - A and C-C pairs. Both proflavine molecules exhibit disorder. In each... 

C2 Z = 4 Dx = 1.41 R = 0.102 for 4,115 intensities. The structure is a 3 2 complex of proflavine and CpG. The asymmetrical unit contains one CpG molecule, 1.5 proflavine molecules, 0.5 sulfate ion, and 11 5 water molecules. Two CpG molecules form an antiparallel, Watson-Crick, miniature duplex, with a proflavine intercalated between the base pairs through the wide groove. The double helix has exact (crystallographic), two-fold symmetry, and the crystallographic, two-fold axis passes through the C-9-N-10 vector of the intercalated proflavine. A second and a third molecule of proflavine are stacked on top of the C - G pairs ... 

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

Acridine derivatives, such a proflavine (5) and acridine orange (6) (Scheme 3), are a second class of intercalative DNA guest molecules for which binding dynamics have been extensively studied. 

Additional evidence that one or both of the mechanisms are operative comes from the data obtained on Cs+-saturated clays. Now, the individual clay platelets in the aggregates are separated by at most a monolayer of water (10) The proflavine molecules adsorb preferentially in that interlamellar space to replace the water and to form a monolayer of proflavine molecules. No dimers are formed, except for a small amount on the external surface of the aggregates, and the quantum yield is almost independent of the loading. 

Assume a random distribution of the adsorbed proflavine molecules over the surface. The surface areas are 775, 819 and 133 m2/g for H, L and BS respectively. The number for BS is obtained from Van Olphen and Fripiat (12). The two other numbers are calculated for average particle sizes of 300 nm and 30 nm for H and L respectively. The former is the size fraction of H used for our experiments, the latter is taken from Van Olphen and Fripiat (12). The surface volume is taken as the... 

Figure 7. The data indicate that about 0.6% of the original ester groups in the PnBA film weathered for 2500 hours were able to bind one molecule of proflavine hemisulfate. Since there are several literature values for the binding ratio, this estimate of 0.6% corresponds to a minimum of 1.8% and a maximum of 12% of carboxylic acid groups in the film. Since the film did not swell in the experiments and proflavine is a bulky molecule, it is quite possible that the dye did not penetrate the film completely. Therefore, the actual content of carboxylic acid may be higher.

Fig. 10.7 Sketches representing the secondary structure of normal DNA (left) and DNA containing intercalated proflavine molecules (right). The helix is drawn as iewed from a remote point, so that the base-pairs and the intercalated proflavine appear only in edgewise projection, and the phosphate deoxyribose backbone appears as a smooth coil. (Redrawn from Lerman, 1964b.)...

Fig. 2. Position of intercalated acridine molecules. 1 A, structure of normal DNA B, structure of DNA containing intercalated proflavine molecules. (After Ler-man, L. S., 1964.) 2 A, the relative position of an acridine nucleus and a base pair in the intercalation model according to Lerman (1964) b, the relative position of the acridine nucleus and the purine of a base pair in the intercalation model of...

A good understanding of the properties of water is thus essential as we move to more complicated systems. We have been involving in the study of aqueous solution of many important biological molecules, such as acetylcholine, Gramicidin, deoxydinucleoside phosphate and proflavin, and DNA, etc., first at the Monte Carlo level and slowly moving to the molecular dynamics simulations. We will discuss some of the new results on the hydration structure and the dynamics of B- and Z-DNA in the presence of counterions in the following. 

Thus complete intercalation of the aromatic PAH between the bases of DNA, in the manner described above for flat molecule such as proflavine, did not seem to be a likely mechanism for the carcinogenic action of these compounds. Since alkylation and intercalation are not simultaneously possible for steric reasons, and since one molecule is wedge-shaped and the other is flatter, it was considered more likely that the action of these compounds arose from their alkylating ability they could alkylate a base of DNA and then, since the bulky aromatic hydrophobic group would possibly not remain protruding into the hydrophilic environment, it is possible that the aromatic PAH group could then lie in one of the grooves of DNA. 

When the stretched DNA-lipid film was soaked in an aqueous solution of ethidium bromide (itmax = 480 nm) for a day at room temperature, the transparent film turned red (itmax = 520 nm) and the aqueous solution became clear (Fig. 9a). Thus, the ethidium intercalated completely between base pairs of the DNA film. When the film was moved into the new aqueous buffer solution, the intercalated dye molecules were hardly removed from the film at least for a day. Similar intercalation behavior into the film was observed for other dyes such as proflavine, acridine orange, and safranine T [14-17]. 

Cationic amphiphiles 2Ci8-glu-N spread on pure water, in the solution of 10 xM DNA containing 10 xM intercalating dyes (proflavine). The dye-intercalated DNA anions were expected to adsorb to the cationic lipid mono-layer due to electrostatic interactions and was transferred to a hydrophobized glass plate at a surface pressure of 35 mN m at 20 °C. From a moving area of a barrier, two layers of the monolayer were confirmed to be transferred in each one cycle (Y-type deposition). When the QCM plate was employed as a transfer plate, the transferred mass could be calculated from frequency decreases (mass increase on the QCM) [29-31]. It was confirmed that 203 10 ng of two lipid monolayers and 74 5 ng of DNA strands were transferred on to the substrate per dipping cycle, which means ca. 95% of the monolayer area was covered by DNA molecules. 

Fig. 14. Schematic representation of light-driven (2e + 2H+) symport across a membrane via the quinone carrier molecule vitamin Kj and its hydroquinone form proflavine (PF)-sen-sitized photoreduction of methyl-viologen MV2+ in the RED phase, yields the reducing species MV+, with simultaneous oxidative decomposition of EDTA used as electron donor the OX phase contains ferricyanide as electron acceptor [6.49].

Transfer RNA (tRNA) molecules mediate translation of the nucleic acid genetic code into the amino acid building blocks of proteins, thus ensuring the survivability of cells. The dynamic properties of tRNA molecules are crucial to their functions in both activity and specificity. This chapter summarizes two methods that have been recently developed or improved upon previous protocols to introduce fluorophores to site-specific positions in tRNA. One method enables incorporation of fluorophores carrying a primary amine (such as proflavin or rhodamine) to dihydrouridine (D) residues in the tRNA tertiary core, and a second method enables incorporation of pyrroloC and 2-aminopurine to positions 75 and 76, respectively, of the CCA sequence at the 3 end. These site-specific fluorophore labeling methods utilize tRNA transcripts as the... 

In addition to proflavin and rhodamine, the photobleaching-resistant Cy3 and Cy5 fluorophores are also frequently used in single-molecule experiments and have been incorporated in the form of hydrazide derivatives into tRNAs via D residues (Pan et al., 2009) (Fig. 4.2). However, quantitative uptake of these hydrazide dyes requires modification of three reaction parameters higher concentrations of the hydrazide dyes (40 mM) than that required for proflavin or rhodamine (22 mM), pH 3.7 rather than pH 3.0, and 2 h reaction time instead of 45—90 min. The requirement of higher concentration is to promote formation of hydrazide adduct, while the slighdy elevated pH prevents hydrolysis of the adduct, which is acid labile. Thus, while the labeling method can be adapted to incorporate new fluorophores besides proflavin and rhodamine, it is prudent to systematically evaluate for the fluorophores under consideration for coupling efficiency as a function of dye concentration, pH, and reaction time. 

As a comparison, fluorescent labeling of tRNA with PyC is achieved in one step by the CCA enzyme, and thus is conceptually and technically simpler than labeling of tRNA with proflavin, rhodamine, or Cy3 and Cy5-hydrazides via D residues. However, the fluorescence emission intensity of PyC is not as high as those of the other fluorophores and thus may not be suitable for single-molecule experiments. Nonetheless, enzymatic labeling of tRNA with PyC is easy to implement and should be applicable to all tRNA sequences (both wild type and mutants), which can be generated by in vitro transcription without the requirement for a specific modification or for native tRNA species. 

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