Cytidine dissociation

A less ambiguous situation prevailed when cytosine and cytidine were compared. The former possesses a pK for the ammonium function (4.60) and an acidic pKa (12.16) for the 2-hydroxyl group. The nucleoside also shows two dissociations (4.22 and 12.3). Since the higher dissociation constant was stated109 to be due to the sugar moiety, it followed that the pyrimidine portion, itself, shows no acidic dissociations in this nucleoside. The authors109 concluded, therefore, that cytidine (and uridine) bear the sugar radical on position 1 rather than 6 of the base. 

So far, two different mechanisms of single strand break formation based on adiabatically stable anions have been proposed. The first mechanism, suggested by the Leszczynski group, assumes the formation of stable anions of 3 - and 5 -phosphates of thymidine and cytidine in which the cleavage of the C-O bond take place via the SN2-type process. The second reaction sequence, proposed by us, starts from the electron induced BFPT process followed by the second electron attachment to the pyrimidine nucleobase radical, intramolecular proton transfer, and the C-O bond dissociation. In both mechanisms the bottleneck step is associated with very low kinetic barrier which enables the SSB formation to be completed in a time period much shorter than that required for the assay of damage. 

Schematic representation of the subunit structure of aspartate transcarbamoylase and its dissociation into catalytic and regulatory subunits by mercurials, which can be further converted to inactive monomeric subunits by strong denaturing agents (e.g., sodium dodecyl sulfate). The native enzyme consists of two catalytic trimers placed one above the other, along with three dimeric regulatory subunits surrounding the catalytic trimers in an equatorial plane (a). Substrate maintains the enzyme in the catalytically more active relaxed (R) conformation, while cytidine tripho.sphate maintains it in the catalytically less active taut (T) conformation (b). [Reproduced, with permission from E. L. Smith, R. L. Hill,...

The kinetics of complex formation between Ni(II) and ortho-phosphate, ribose monophosphate and cytidine monophosphate (CMP) in water have been reported.The results are consistent with an/ mechanism involving protonated (HL ) and unprotonated (L ) ligands, and rate constants for reaction with L and HL" are about 1.5 x 10 dm mol s and 2.3 x 10" dm mol" s respectively, for all three systems. The cytidine ring appears to exert no effect on the binding of Ni(II) to CMP. The rate parameters have also been reported for the reaction of nickel(II) with 4-phenylpyridine and isoquinoline in water-r-butanol mixtures. Rate parameters for the dissociation of the isoquinoline and thiocyanate complexes of Ni(II) in 1-propanol, and of the former in ethanol and in water, are accommodated within an Id mechanism, and Tanaka has commented further on the relationships between the activation enthalpies for the dissociation of the same two complexes and the Gutmann donor number of the solvent. 

The first mechanism for LEE-induced SSBs was proposed by Simons and coworkers employing a Hartree-Fock (UHF) level of theory and 6-31+G basis set (Barrios et al. 2002). In their study, they considered 3 -cytidine mono phosphate (3 -dCMPH) as a model of DNA and studied the ground-state potential energy surfaces (PESs) of the bond dissociation in the... 

In this situation, two different polypeptide chains interact to form a new specific complex, whose biologic activity can be modified by ligands that bind to the precursor subunits. This type of regulation has been extensively studied for the aspartate transcarbamylase of E. coli (Gerhart, 1970). This enzyme catalyzed the initial step in the synthesis of cytidine nucleotides it is allosterically inhibited by CTP and shows positive cooperativity for substrate. It may be dissociated by mercurials into catalytic subunits, which are insensitive to CTP and which exhibit hyperbolic kinetics for substrate, and into regulatory subunits which bind CTP. 

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