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Cytidine deaminase is known as an important enzyme responsible for the hydrolytic deamination of cytidine, which is applied as a key step to the conversion of the precursor of the cancer drug to an active form in the living body. Cytidine with water is efficiently converted to uridine with ammonia in the cleft of cytidine deaminase. In this work, the(More)
A critical role is traditionally assigned to transition states (TSs) and minimum energy pathways, or intrinsic reaction coordinates (IRCs), in interpreting organic reactivity. Such an interpretation, however, ignores vibrational and kinetic energy effects of finite temperature. Recently it has been shown that reactions do not necessarily follow the(More)
DNA interstrand crosslinks (ICLs) are the primary mechanism for the cytotoxic activity of many clinical anticancer drugs, and numerous strategies for forming ICLs have been developed. One such method is using crosslink-forming oligonucleotides (CFOs). In this study, we designed a 4-amino-6-oxo-2-vinylpyrimidine (AOVP) derivative with an acyclic spacer to(More)
We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which(More)
To investigate the dominant factors that allow a reproducible nuclear reaction in D-Pd systems, the initial electric resistance and the hardness of the Pd cathode have been examined for excess heat generation and the excess neutron emission in LiOD-Pd electrolysis cells. Two background (control) runs and one foreground run with the Pd cathode of high(More)
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