Intercalation ethidium

Fig. 5 Charge transfer occurs through the DNA /r-stack and is strongly dependent on minor base stack perturbations. Photoinduced electron transfer is observed from tethered intercalated ethidium to a rhodium intercalator bound to DNA up to 30 A away. The efficiency of electron transfer is drastically reduced in the presence of a stacking disruption, here a single base-pair mismatch... 

Oxidative repair is not a unique feature of our Rh(III) complexes. We also demonstrated efficient long-range repair using a covalently tethered naphthalene diimide intercalator (li /0 1.9 V vs NHE) [151]. An intercalated ethidium derivative was ineffective at dimer repair, consistent with the fact that the reduction potential of Et is significantly below the potential of the dimer. Thymine dimer repair by a series of anthraquinone derivatives was also evaluated [151]. Despite the fact that the excited triplets are of sufficient potential to oxidize the thymine dimer ( 3 -/0 1.9 V vs NHE), the anthraquinone derivatives were unable to effect repair [152]. We attribute the lack of repair by these anthraquinone derivatives to their particularly short-lived singlet states anthraquinone derivatives that do not rapidly interconvert to the excited triplet state are indeed effective at thymine dimer repair [151]. These observations suggest that interaction of the dimer with the singlet state may be essential for repair. 

Excitation Transfer between Intercalated Ethidium Dyes... 

Fluorescence depolarization by excitation transfer between intercalated ethidium dyes was originally studied in attempts to determine their unwinding angle/65, 156l5S i The total anisotropy was assumed to be given by a simple... 

Effect of Intercalated Ethidium on the Torsion Constants of Linear and Supercoiled DNAs... 

Up to r = 0.10, intercalated ethidium has no significant effect on the torsion constant of linear DNAs, as indicated in Figure 4.17.(223) Together... 

Figure 4.18. Torsion constant a of supercoiled pJMS2 DNA versus ethidium/base pair, denoted by EB/BP. The lilted symbols are torsion constants obtained after correcting for the effects of energy transfer. The open symbols are the apparent torsion constants obtained from FPA data without taking excitation transfer into account. Even after correcting for excitation transfer, the torsion constant of this supercoiled DNA decreases appreciably with increasing intercalated ethidium, in contrast to linear DNAs.

The rotational dynamics of nucleosomes containing (146 2)-bpDNA bound to core particles was studied by FPA(21,59 ° 235-1 of intercalated ethidium and by TPD(62) of intercalated Methylene Blue. These studies yield strong evidence that DNA wrapped around the histone core particle exhibits... 

Among these methods, hydrodynamic measurements of sedimentation coefficients and viscosity are classical [43,47]. The insertion of a true intercalator (ethidium bromide for example) between the stacking of bases produces... 

I. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4,6-Diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study. J. Am. Chem. Soc. 124, 3366-3376 (2002)... 

Fluorescence-based indicator reactions can also be coupled to measurements of enzymatic activity. For example, very sensitive assays of endonuclease activity can be performed using as a substrate complexes of double stranded DNA containing intercalated ethidium bromide, which is strongly fluorescent. On cleaving or nicking the DNA, the intercalated ethidium is released into the solution causing a pronounced decrease in fluorescence intensity. 

There have been numerous investigations of the fluorescence quenching of intercalated ethidium (ET+ Table 5) by intercalated or groove bound quenchers [128-... 

Fig. 2. Degradation kinetic of lipoplexes obtained with stable lipid 3 and pH labile lipids 2 and 4 at pH 5, and charge ratios 1.7 and 6. DNA release induced by degradation is measured by the % of fluorescence of intercalated ethidium bromide at 590 nm " 260 nm (100% refers to naked DNA)...

RADACK may also account for the experimentally observed reduced probability of getting a damage at the site of binding of a minor groove ligand that has a preference for a specific sequence (a natural polyamine [16] ora therapeutic radioprotector, Ethyol [17]) as it does for the experimentally observed effect of an intercalator (ethidium bromide) [18]. 

Porphyrins bound to the minor cleft have large effects on the DNA-en-hanced fluorescence of intercalated ethidium ions (E ). Cationic porphyrins are... 

Straight SOmer and A5-bulge bent SOmer/ intercalated ethidium bromide Series of oligos... 

G-quadruplex DNA can convert to the duplex form in the presence of its complementary strand [82]. Such a conformational change can also be detected using P4 [83]. The overall strategy is illustrated in Scheme 1.18. The intercalator ethidium bromide (EB) is introduced into the assay solution. Electrostatic interactions between G-quadruplex-Fl and P4 keep them... 

Ashikawa, I., Kinosita, K., Dcegami. A.. Nishimura, Y, l ibot, M.. Watanabe, K., Iso, K., and Nakano. T. 1983, Inlemal motion of deoxyribonucleic acid in chromatin. Nanosecond fluoiescencestud-ies of intercalated ethidium, fiiochemutry 22 6018-6026. 

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