Cytidine conformation

The ac" C nucleoside is found at the wobble position of methionine tRNA from E. coli as well as glutamine, glutamate, lysine, proline, and serine tRNAs in archaea. Kawai et al showed that ac" C strongly favors the 3 -endo conformation, and that this conformational preference is reinforced by simultaneous 2 -OMe to form the ac Cm nucleoside found in tRNAs from hyperthermophilic archaea. The presence of N-acetylated cytidine in organisms growing above 100 °C is somewhat remarkable given the hydrolytic lability of this functionality. In light of the dramatic effects that ac" and f modifications have on the cytidine conformational preference, these modifications could have applications for RNA duplex stabilization similar to that shown recently for s U. ... 

FIGURE 11.11 The common ribonucleosides—cytidine, uridine, adenosine, and guanosine. Also, inosine drawn in anti conformation. 

High-frequency, p.m.r. spectroscopy has proved to be an extremely important tool in studies of the structures, conformations, and inter-and intra-molecular base-stacking interactions of nucleosides and nucleotides. The temperature dependence of the chemical shift of the base proton at position 6 (H-6) has been studied at 220 MHz for uridine (36), cytidine (38), and a number of their mono- (37, 39) and... 

The crystal structure of l-(/3-D-erythrofuranosyl)cytidine, the des(hydroxymethyl) analog of /3-cytidine, has been determined and used to correlate the preferred conformations of furanoses in solution with those in the solid state. Conformational similarities and differences of tetrofuranoses vs. pentofuranoses have been charted as well <2007AXCol37>. 

The use of paramagnetic ions to examine the binding sites and solution conformations of nucleosides and nucleotides is becoming very widespread. Studies that describe the complexing of a variety of nucleosides and nucleotides with paramagnetic ions involve the use of Mn(ii), (749-751) Cu(ii), (750, 752-754) and lanthanide ions. (755) Mn " ions appear to bind to multiple sites on purine and pyrimidine nucleosides (749) whereas the phosphate group is the primary binding site on monophosphate nucleotides. (750) relaxation studies indicate that Cu " ions bind to N-3 of 5 -cytidine monophosphate (5 -CMP). In contrast to cytidine [59], adenosine [60] appears to have... 

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,...

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