C3 -endo-sugar pucker

Ajnti base pairs with N-lH-O-6 and N-6H-N-7 H-bonds, respectively (203). The ps-DNA formed by d(G-A)25 has a of 40°C and shows very little fluorescence upon staining with EtBr. In contrast to the d(A) -d(T) ps-DNA, d(G-A) ps-DNA displays C3 -endo sugar puckering and apparently shares some essential structural elements with left-handed Z-DNA. 

It can be seen that alkylation has changed the sugar-base conformation (distant from the site of alkylation) from anti (as in deoxyadenosine and in B-DNA) to syn (as in alkylated deoxyadenosine and in some bases in Z-DNA). The sugar puckers are either C2 -endo or C3 -endo. A second structural feature of great interest in these crystals is that the more planar anthracene portion of the PAH is stacked between adenine residues of other molecules throughout the crystal. The highly buckled region of the PAH does not take part... 

CPMAS solid-state NMR has been used to investigate the dependence of sugar chemical shifts on specific conformational parameters of a variety of ribonucleotides and ribonucleosides. The distinct effects of sugar puckering on the Cl, C4, and C5 resonances of Cj endo (S type) and C3 endo (N type) furanoid conformations allow us to separate them into two groups. 

In order to preserve optimal stability in the hybridization of RNA by sugar-modified oligonucleotides, nucleosides substituted at the 2 -position must retain a C3 -endo puckered conformation. To this end, the 2 -0- 2-[iV,N-(dimethylamino)oxy]ethyl and the 2 -0- 2-[Ar,lV-(diethylamino)oxy]-ethyl 3 -phosphoramidite derivatives of thymidine (38a, 38b) have been synthesised. The nucleoside precursors were prepared from a phthalimido-derivative obtained from 2,2 -anhydro-5-methyluridine which had been treated, after appropriate protection, with a borate ester generated in situ and then reacted with PPha, DEAD and AT-hydroxyphthalimide. The incorporation of (38a) and (38b) in oligonucleotides and oligodeoxynucleotides resulted in high binding affinity for... 

Sugar pucker C3 -endo C2 -endo C3 -endo for dG, C2 -endo for others... 

Sugar pucker The furanose rings are twisted out of plane in order to minimize nonbonded interactions between their substituents. This puckering is described by identifying the major displacement of C2 and C3 of pentose from the median plane of CT—04 —C4. Thus if the endo-displacement of C2 is greater than the exodisplacement of C3, the conformation is called CT-endo and so on. The endo-face of the furanose is on the same side as C5 and the base the exo-face is on the opposite face to the base. 

There are two preferred orientation anti and syn) of the base with respect to the sugar, as determined by steric restrictions during the torsion (%) about the CT—N glyco-syl bond. The sugar is nonplanar, and two of its common puckering modes are C2 -endo (S-type) and C3 -endo (A-type). The secondary stracture of DNA can be described by a number of parameters that define the helix (Dickerson et al 1989) ... 

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