Multiple conformations, nucleotides

The fluorescence decay of dinucleoside monophosphates containing the modified base ethanoadenine (EAD) (see Table 4) and the natural bases guanine and uracil have been investigated by Kubota et al. [31c]. The fluorescence quantum yields are lower for the conjugates than for the nucleotide of EAD (<0.1 versus 0.52). The observation of multiple exponential fluorescence decay was attributed to multiple conformations. A small component with a decay time similar to that of unmodified EAD was attributed to an extended conformation and two shorter components to loosely stacked folded conformations. While the mechanism of fluorescence quenching was not addressed, an electron transfer mechanism in which singlet EAD can serve as an electron acceptor (with guanine) or electron donor (with uracil) is... 

Multiple Conformations Ensembles. When multiple conformations are present, the problem rapidly becomes underdetermined. For example, if a nucleotide can exist in two major conformational states, with x(N)P(N) and x(S)P(S) where the glycosidic torsion angles in the N and S sugar states are not equal, each conformation will have its own characteristic NOEs and coupling constants. For n bases, there are 2" conformations, and the contribution of each one to the ensemble will depend on its population. Even for a dinucleotide, there are at least 4 conformations (viz. SS, SN, NS, NN), which multiplies the number of structural parameters to be determined fourfold, plus four equilibrium constants. There are not enough independent NMR data to determine all of these parameters and the problem is underdetermined. In this situation, the best that can be hoped for is to derive a set of structures that in some way represent the ensemble of structures that is present in solution. 

As described in Section III, the conformation of each actin monomer or each tubulin monomer in F-actin or microtubule is more or less different depending on the environmental condition and the species of bound nucleotides and bound cations. Does each monomer in the polymer assume the same conformation in the same environmental condition even when it has the same bound nucleotide and divalent cation The monomer may take multiple conformations. 

The second difference concerns the conformation about the thymine-deoxyribose bond of dTTP, which in the ternary complex has the configuration corresponding to a nucleotidyl unit in the product, i.e. double helical DNA. This may represent an error-preventing mechanism 338 The RNA polymerases are more complex.339 They contain two Zn2+ per molecule, although additional zinc may bind at the Mg2+ site with inhibition. There may well be multiple roles for Zn2+, both structural and catalytic. The two sites in the enzyme from B. subtilis have different340 affinities for Zn2+, in accord with this proposition. The enzyme from E. coli has at least five subunits. Zn2+ is located on the subunit which binds DNA and on the subunit on which the initiation and elongation nucleotide binding sites are located.341... 

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... 

Chloroplasts of land plants contain multiple identical circular double-stranded DNA molecules, whose size, according to different data, varies from 120 to 160 or to 220 kb. In the population of cpDNA molecules obtained by chloropiast lysis, monomeric circles prevail (-60% of all circular DNA molecules in tobacco). There also ate oligomeric forms, which are concatemers or head-to-tail associates that most probably arose during DNA recombination and/or replication, as well as atypical molecules, presumably replicative intermediates. Accordingly, the chloropiast genome is not uniform and exists in the cell as a DNA population heterogeneous in molecule size and conformation. The first complete nucleotide sequences of cpDNA were determined in 1986 for tobacco ... 

Extensive synthetic efforts have been made into the preparation of highly complex nucleosidic building blocks, whereby functionalization and conformational restriction were introduced via multiple ring incorporation into the glycosidic framework of the nucleotides. The introduction of such complexity has come at a price as these compounds often require lengthy synthetic sequences to achieve both chemoselectivity and stereochemical definition. 

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