Base-pair overlaps

Base Pair Overlaps The chemical shifts in the duplex state,... 

Figure 3). These upfield shifts reflect the base pair overlap geometries in the duplex state and result predominantly from ring current contributions due to nearest and next-nearest neighbor base pairs (33,34) These contributions can be computed for the B-DNA overlap geometry and are compared with the experimental upfield chemical shifts on duplex formation of poly(dA-dT) and the related synthetic DNA pol.y(dA-dU) in Table II.

The chemical shifts are similar at high temperature and differ by uO.l ppm at the lower temperature (Figure 12). This suggests that similar base pair overlaps are observed for poly(dA-dT) in 1 M Na+ and 1 M TMA+ as monitored at the thymidine H-3 proton located in the center of the base pair. 

The observation of selective complexation shifts in the nucleic acid resonances of the synthetic DNA demonstrate a change in the glycosidic torsion angles of the adenosine and thymidine residues and a minimal perturbation in the base pair overlaps on addition of netropsin. These structural perturbations at the antibiotic binding site are propagated to adjacent antibiotic-free base pair regions at low netropsin concentrations. 

If the fluorescence spectra of the acid base pair overlap, then the measured fluorescence intensities of BH+ (y) and B (./ ) must be corrected for the intensity component due to the other form. The true fluorescence intensities (0 and (j) ) are related to the measured intensities according to the equations ... 

Group I intron phosphotransesterification reactions are carried out by a conserved active site that contains a set of imperfect double helices named PI through P9. (See Figure 6.4.) P1-P9 helices are organized into three domains P1-P2, P4-P6, and P3-P9. Specifically, the Tetrahymena thermophila intron contains two sets of coaxially stacked helices that overlap to create the active site. These helices reside in two domains of approximately equal size P4-P6 and P3-P9. P domains are defined as base-paired regions, whereas J domains... 

The absorbance maximum of phenols is increased by the addition of base and formation of the phenolate ion, with an associated absorbance shift to longer wavelength (a bathochromic or red shift), whilst the absorbance maximum of anilines is decreased by the addition of acid, which causes protonation of the amine and loss of the lone pair overlap with the K-system, leading to an absorbance shift to shorter wavelength (a hypsochromic or blue shift). 

One of the best-documented examples occurs in translation of the mRNA for the overlapping gag and pol genes of the Rous sarcoma virus (see Fig. 26-31). The reading frame for pol is offset to the left by one base pair (—1 reading frame) relative to the reading frame for gag (Fig. 1). 

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