Intercalation sites

The most commonly used dye in fluorescence studies on nucleic acids is ethidium bromide. The dye has broad excitation bands centered around 280 and 460 nm and a strong emission around 600 nm. When the dye hinds to DNA by an intercalative mechanism, its emission is greatly enhanced and slightly shifted in wavelength. In the simplest case with ethidium bromide saturating intercalating sites,... 

In the case of solutions based on a solvent such as propylene carbonate (PC), the failure of graphite electrodes is attributed by some researches to the exfoliation of the graphite particles due to cointercalation of PC molecules with the Li ions.14,22 The difference between ethylene carbonate (EC) and PC in this respect may, according to this approach, be attributed to the higher ability of PC molecules to solvate Li ions.23 Hence, cointercalation of PC molecules takes place because their desolvation from Li ions, which migrate from solution phase to the intercalation sites in the graphite,... 

Meehan and Bond (23) on the other hand, have taken an opposite view, namely that k3I1(C) k3I(C), while k3II(T) k3I(T). Thus, in this view, the hydrolysis occurs at external binding sites, while covalent binding occurs at intercalation sites. Furthermore, they reject the common intermediate model (Equation 2) on the basis of their belief that the rates of reaction for tetraol formation and adduct formation and the ratio of the products should be the same in such a model. While these rates of reaction are the same and the product ratios are observed to be different, this is fully consistent for a set of parallel pseudo-first order reactions involving a common intermediate (29) as pointed out above. Thus, the data of Meehan and Bond does not demonstrate the validity of the two-domain model (23). 

Receptor sites. The intercalation and kinked sites in DNA used in this study are listed in Table V. Three theoretically determined intercalation sites (I, II and III) permit the study to be conducted with the DNA unwound by 7°-12°, lU-l8° and 25°-32° with parallel base pairs separated by 6.76 A and with alternating (a) sugar puckers (67,68) Attention will be confined to site I because it was found to be the most favorable in the present studies. Several kink (K) sites have been identified (66). The constraint that proper hybridization exists about N2(g) and CIO of BPDEs stimulated an investigation in kinked DNA. In an idealized structure the pyrene moiety is approximately parallel to one of the base pairs as shown... 

Dimethyl-5-methoxyangelicin 11 and 4,4 -dimethyl-5-methoxypsoralen 12 were added separately to 12 synthetic oligonucleotides, and their interaction and subsequent photoaddition reaction on UVA irradiation was studied <2000PCB4992>. The kinetics constant of the overall photoaddition process was determined accurately, the different intercalation sites were identified, and the value of the kinetics constant relative to each type of site was determined. 

Bisbenzimidazoles (for a review, see Martin 1998) protect cells against ionizing radiation (Denison et al. 1992 Lyubimova et al. 2001). Bisbenzimidazoles such as Hoechst 33258 strongly bind to the minor groove of B DNA (Pjura et al. 1987 in a dodecamer the ATTC region is the preferred intercalating site). 

Figure 2 shows the initial equilibrated intercalated state. The DNA sequence is d(GCGCACGTGCGC)2- The intercalated structure s geometry is that of the B-DNA except for the 5th to 7th base pairs (A5 to G7), which stay close to the crystal structure used for the starting conformation, with a root mean square deviation of 3.2 A for all the heavy atoms of those three basepairs. In this sequence, daunomycin is in contact with the strongest binding triplet sequence (A/T)CG [18,19]. Moreover, due to the chosen sequence of the DNA, the intercalation site is flanked by the same sequence of base-pairs in either direction, eliminating any related orientational preference of... 

Overlap Geometry A schematic representation of the proposed overlap geometry for proflavine intercalated into a deoxy pyrimidine(3 -5 )purine site is presented below with the (o) symbols representing the location of the phenanthridine ring protons. The mutual overlap of the two base pairs at the intercalation site involves features observed in the crystal structures of a platinum metallointercalator miniature dC-dG duplex complex (55) and the more recent proflavine miniature dC-dG duplex complex (48), as well as features derived in a linked-atom conformational calculation of the intercalation site in the proflavine DNA complex (51). [4]... 

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