Nucleosides, nucleotides conformation

Fig. 17.4. Description of the main sugar conformations in nucleosides, nucleotides, and nucleic acids [522]...

Conformation 2.42, P = 175°, is rather close to The maximum torsion angle is still between 2 and 3, -42°. The fact that the same molecule can have two different conformations in the same crystal is in itself indicative of their small energy difference. All the same it is unusual and nucleosides/nucleotides are divided equally between 0° < P < 36° and 144° < P < 180° with few exceptions. 

This notation will be explained by an example taken from the chemistry of nucleosides/nucleotides, by far the most important family of furanosides (see Section 3.4). The nucleosides are glycosidic combinations with a heterocyclic base and a /3-D-ribofuranosyl or 2-deoxy-)3-D-cryr/iro-pentofuranosyl residue. The example chosen is the synthetic nucleoside 5-iodouridine. We can observe two different conformations of this molecule in the crystalline form, close to 72 (2.41) and Tj (2.42), respectively. The maximum torsion angle is between the 2 and 3 positions. In order for P to be close to 0, we will therefore choose T2 = Oq (Fig. 2.10) and consequently for 0. .. 0, the values T3, T4, Tq, and Ti, respectively. Knowledge of the two torsion angles allows us to calculate and P. The P angle has the character of a phase and is a measure of the flattening of the... 

The concept of the anomeric effect in systems O-C-N is of great importance in chemical behavior of nucleosides, nucleotides, and nucleic acids since it controls the conformation of ribofuranosyl (or deoxyribofuranosyl) ring and with it the reactivity of the W-glycosidic bond. 

Thibaudeau C, Chattopadhyaya J (1998) The information transmission from the nucleobase drives the sugar-phosphate backbone conformation in the nucleotide wire. Nucleosides Nucleotides 17 1589-1603... 

Nucleosides, Nucleotides, Derivatives, and Related Compounds. — 5-Substituted uracils were examined for conformational dependence on the substituents, uridine 5 -phosphate disodium salt, 2 -deoxyuridine 5 -phosphate disodium salt, " 6-methyl-2 -deoxyuridine, 5-C-acetyl-2 -deoxyuridine, dihydrouridine 3 -phosphate potassium salt, 5-hydroxymethyl-2 -deoxyuridine, 4-thio--uridine, 2,5 -anhydro-2, 3 -0-isopropylidene-2-thiouracil, 2,2 -an-hydro-1 - 3-D-arabinofuranosyl-2-thiouracil. ... 

CO-OPERATIVE CONFORMATIONAL PROPERTIES OF NUCLEOSIDES, NUCLEOTIDES AND NUCLEOTIDYL UNITS IN SOLUTION... 

Nucleosides, Nucleotides, Derivatives, and Related Compounds.—(Data derived from J T-ray analysis of 99 compounds containing the JV-jS-D-pentofuranosyl unit have been correlated. The questions of conformational interchange via ring flattening or pseudorotation and the orientation of groups bonded to C-5 were considered in detail. )... 

A brief review of ultrasonic absorption studies of aqueous solutions of biological compounds (amino-acids, bases, nucleosides, nucleotides, polypeptides, proteins and nucleic acids) in relation with stacking, conformational transitions and proton transfers is presented. 

Kazimierczuk Z, Dudycz L, Stolarski R, Shugar D (1981) Synthesis and conformation of halogeno benzimidazole nucleosides-fluoro-derivative and iodo-derivative. J Carbohydr Nucleosides Nucleotides 8(2) 101-117... 

Molecular conformation of 2 -deoxy-2 -methylidenecytidine a potentially antineoplastic nucleoside. Nucleosides Nucleotides, 11 835 (1992). 

The Fe-protein has the protein fold and nucleotide-binding domain of the G-protein family of nucleotide-dependent switch proteins, which are able to change their conformation dependent on whether a nucleoside diphosphate (such as GDP or ADP) is bound instead of the corresponding triphosphate (GTP or ATP). However, nucleotide analogues, which induce the conformational switch of the Fe-protein, do not allow substrate reduction by the MoFe-protein, nor does reduction of the MoFe-protein by other electron-transfer reagents (whether small proteins or redox dyes) drive substrate reduction. Only the Fe-protein can reduce the MoFe-protein to a level that allows it to reduce substrates such as... 

The conformations of the furanose ring in 250 nucleoside and nucleotide structures were analysed by Bartenev et al. (1987). These authors made the assumption, referred to above, that intermolecular interactions have a random effect on the structure in the crystal, and that the probability JVg of a structure crystallizing in a non-ground-state conformation is the same as the probability of it arising in thermal equilibrium at ambient temperature T in solution (6). (A difficulty arises immediately with the definition of the temperature, because structural parameters for molecules in crystals are... 

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