Grooved asymmetrically

Figure 7.4 The edges of the base pairs in DNA that ate in the major groove are wider than those in the minor groove, due to the asymmetric-attachment of the base pairs to the sugar-phosphate backbone (a). These edges contain different hydrogen bond donors and acceptors for potentially specific interactions with proteins (b).

The sugar-phosphate backbone is represented by connected circles in color and the base pairs as blue planks. Four base pairs are shown from the top of the helix to highlight how the grooves are formed due to the asymmetric connections. The position of the helix axis is marked by a cross. 

C2 Z = 4 Dx = 1.41 R = 0.102 for 4,115 intensities. The structure is a 3 2 complex of proflavine and CpG. The asymmetrical unit contains one CpG molecule, 1.5 proflavine molecules, 0.5 sulfate ion, and 11 5 water molecules. Two CpG molecules form an antiparallel, Watson-Crick, miniature duplex, with a proflavine intercalated between the base pairs through the wide groove. The double helix has exact (crystallographic), two-fold symmetry, and the crystallographic, two-fold axis passes through the C-9-N-10 vector of the intercalated proflavine. A second and a third molecule of proflavine are stacked on top of the C - G pairs ... 

Fig. 2 A 1.4 A crystal structure reveals that intercalating phi ligands do not disrupt the DNA re-stack. Shown are a the five A-a-[Rh(R,R-dimethyltrien)phi]3+-DNA octamers stacked end-to-end in the asymmetric unit of the crystal, and b a view from the major groove of A-a-[Rh(R,R-dimethyltrien)phi]3+ intercalated in the DNA duplex, 5 -G-dIU-TGCAAC-3. The intercalator is inserted as an additional DNA base step with minimal perturbation of DNA re-stack. Adapted from [51]...

Intercalators with asymmetric substituents, such as the phenyl and ethyl groups of ethidium bromide (21), frequently cause a smaller increase in DNA length than expected from the simple model described above. In such cases these groups are inserted into the minor groove of the DNA helix with concomitant bending of the double helix towards the major groove. This alternative type of complexation is supported by X-ray studies on model systems, 25). 

The CSN architecture shows similarity to that of the lid. Both complexes have an asymmetric arrangement of their subunits and exhibit a central groove structure... 

For symmetric reflections the peak search may now begin. For asymmetric reflections, the specimen must be rotated about its normal until the desired diffraction vector lies in the incidence plane of the beam conditioner. This is normally the diffractometer surface. An accurate knowledge of the orientation of the specimen in two axes is required to set asymmetric reflections this is usually taken from the position of the orientation flat or groove. 

Mixer 76 [M 76] Oblique, Asymmetrically Grooved Micro Mixer-Staggered Herringbone Mixer (SHM)... 

M 75] [M 76] [P 66] Symmetrical grooves produce non-chaotic flows at the optimized asymmetrical groove geometry most of the cross-sectional area is filled with chaotic flow [44],... 

Asymmetric photoisomerization of cyclo-octene was also investigated in supramolecular systems such as native [153] and modified cyclodextrins [154,155], chirally-modified zeolite [156], and DNA grooves [157]. 

In free molecular flow, if gaseous conductance were not independent of the flow direction, a perpetual-motion machine could be constructed by connecting two large volumes by a pair of identical ducts having a turbine in front of one of the ducts. A duct that has asymmetrically shaped grooves on its wall surface could alter the probability of molecular passage in such a way that for a tube of equal entrance and exit areas, the probability of passage would be made directional. 

The orientation of the amino proton attached to the N2 donor on G differentiates the G C and C G base pairs from each other as well as from the A-T and T-A pairs. The latter base pairs can be discriminated by small synthetic molecules that take advantage of both the asymmetric steric structure of the adenine C2-H and the capability of the thymine 02 (with two sets of lone pair electrons) to form an additional hydrogen bond not possible with the pseudo-symmetrically related adenine N3 (37, 38). It is not yet clear whether naturally occurring, DNA-binding proteins use similar principles to distinguish between A T and T A base pairs in the minor groove. 

The trends seen for AA, AT and TA steps are also shared for the whole group of sequences included in the RR, RY and YR populations, respectively. With this in mind, one would predict that AT, GC and E4 are good promoter sequences, because they are formed by an alternation of RY steps that produce the appropriate roll profile, and YR steps, which are the most flexible and thereby easier to unstack and bend. Note that the roll profiles are asymmetric, and they show a greater tendency to bend towards the major groove than towards the minor groove. This would be reflected in the anisotropic bendability which was invoked by Kahn and coworkers to explain cyclization efficiency of DNA minicircles [97]. Where we disagree is in the direction of the anisotropy. They propose that MLP is bent towards the minor groove, and that this equilibrium conformation acts as an inhibitor of the formation of unproductive complexes. 

There are three grooves in triple-helical DNA which can be targeted for binding by ligands either covalently or noncovalently. The third strand of a triplex is positioned asymmetrically in the major groove and the vacant minor... 

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