Nucleotides observed rate constants

The reaction of Ru-pac complexes with purine-base nucleotides other than AMP, showed a linear dependence of the observed rate constant on the concentration of Nu, however, did not reveal any [Nu]-independent ring-closure step as observed in the case of AMP. The kinetic behavior could be rationalized in terms of the reactions outlined in Scheme 6 for which the rate expression is given in Eq. (1). 

For kinetic experiments a stopped flow apparatus (Bio-logic, Grenoble, France) is used where mant-nucleotide and protein are mixed within less than 1 ms. In order to ensure pseudo-first order conditions for the kinetics, either the protein or the nucleotide is in 10-fold or more molar excess. Fluorescence is excited at 366 nm or 295 nm, respectively, and detected by a photomultiplier after passing through a 400 nm cutoff Alter. A single exponential equation is fltted to the time traces yielding the observed rate constant kcbs-... 

There has been continued interest in the radiation chemistry of the purines since early reports on oriented DNA by Graslund et al. [35] which suggest that the main trapping site of one-electron oxidation in DNA is the guanine base. It is remarkable that in aqueous solution, the electron adducts of the purine nucleosides and nucleotides undergo irreversible protonation at carbon with a rate constant 2 orders of magnitude higher than that for carbon protonation of the electron adduct in thymidine [36]. It is therefore important to know the properties of the various purine reduction products and to ask why they have not been observed in irradiated DNA. 

II). These isotope effects are determined from the net amount of cleavage observed at the labeled nucleotide, not from a time-resolved study of the true cleavage rate constant. 

The reaction of hydrated electrons formed by radiolysis with peroxydisulfate yields the sulfate radical anion SO4 which is a strong chemical oxidant (Eqx = 2.4 V/NHE) [50, 58]. The oxidation of both purine and pyrimidine nucleotides by S04 occurs with rate constants near the diffusion-controlled limit (2.1-4.1 x 10 M s ). Candeias and Steenken [58a] employed absorption spectroscopy to investigate acid-base properties of the guanosine cation radical formed by this technique. The cation radical has a pKa of 3.9, and is rapidly deprotonated at neutral pH to yield the neutral G(-H) . Both G+ and G(-H) have broad featureless absorption spectra with extinction coefffcients <2000 at wavelengths longer than 350 nm. This has hampered the use of transient absorption spectra to study their formation and decay. Candeias and Steenken [58b] have also studied the oxidation of di(deoxy)nucleoside phosphates which contain guanine and one of the other three nucleobases by SO4 , and observe only the formation of G+ under acidic conditions and G(-H) under neutral conditions. 

The dynamics of both static and dynamic quenching of the fluorescent singlet states of diazapyrenium salts by nucleotides has been investigated by Brun and Harriman using sub-nanosecond time-resolved transient absorption spectroscopy [88]. Observation of the reduced acceptor DAP+ (Table 5) supports an electron transfer mechanism for fluorescence quenching. Diffusion-controlled rate constants were observed for quenching of DAP + by all four deoxynucleotides. Excitation of... 

BNA (also known as LNA) has been used in TFOs in a pyrimidine motif at neutral pH. The binding constant of the BNA TFO was about 20 times larger than that of DNA as a result of a large decrease in the dissociation rate constant. A 3 -amino-2, 4 -BNA nucleotide has been prepared to introduce N3 -P5 phosphoramidate linkages. It is introduced as a dinucleotide unit (61), and in thermal stability studies was shown to exhibit superior duplex and triplex stability compared to either BNA or DNA, and shows enhanced resistance to digestion by SVPDE. These properties have previously been observed for N3 -P5 phosphoramidate linkages in DNA. ... 

Direct observation of enol ether type radical cations such as are expected to be important in the fragmentation of nucleotide C4 radicals is not possible by the time-resolved laser flash photolysis technique owing to the lack of a suitable chro-mophore. However, it has recently been demonstrated that if such an LFP experiment is conducted in the presence of a triarylamine then any diffusively free enol ether radical cations oxidize the amine to the corresponding highly colored ami-nium radical cation. In this manner the overall rate constant for fragmentation and cage escape may be determined (Scheme 4) [1 Ij. 

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