Hydration spine

On the other hand, according to Kopka et al.158), a zig-zag spine of hydration in the minor groove of the B-DNA 1561 is assumed to be mainly responsible for stabilizing its conformation and a 100% occupancy of the hydration sites in the A + T region has been found. Each first water molecule of this hydration-spine is close to two 0-1 atoms of desoxyribose-rings (Fig. 22). 

Narrow minor groove Hydration spine in the minor groove No amino group in the minor groove Very slow base pair dynamics... 

Sequence dependence of DNA hydration spine of hydration in AT minor groove... 

The mechanism by which the spines grow is fascinating (Fig. 20.4). The initial envelope of hydrate on the cement grains, which gave setting, also acts as a semi-... 

Figure 5-14 (A) Stereoscopic drawing showing two layers of water molecules that form a "spine" or "ribbon" of hydration in the minor groove of B-DNA. The inner layer is shown as larger filled circles water molecules of the outer layer are depicted with smaller dots and are numbered. Hydrogen bonds are shown as dashed lines. (B) Electron density map. (A) and (B) from Tereshko et at.95 (C) Stereoscopic representation of the superimposed electron densities of 101 water molecules observed to hydrate 14 guanine rings found in 14 B-DNA molecules for which high-resolution X-ray structures were available. Positions of 101 water molecules within 0.34 nm from any atom of the 42 guanines are plotted. From Schneider and Berman.94...

For the Tar—Tar kissing loops, the P—B calculations are unable to discern their propensity to accumulate counterions accumulation at the loop—loop interface (data not shown). This is because the fully hydrated ions as defined by the Stem layer cannot penetrate into the central cation binding pocket (data not shown). Similarly, the axial spine of counterion density observed in the A-RNA helix (Fig. 20.5) is not captured by the P—B calculation (Fig. 20.7). No noticeable sequence specificity is observed in the counterion accumulation patterns in the P—B calculations, even though the sequence effects are explicitly represented in the P—B calculation through the appropriate geometry and assignment of point-charges. This is because the sequence specificity observed in the molecular dynamics simulations usually involves first shell interactions of base moieties with partially dehydrated ions, which cannot be accurately represented in the P—B framework. 

Monte-Carlo simulations have been made of the known water structure in crystalline serine monohydrate, arginine dihydrate homoproline tetrahydrate [331], deoxycytidylyl-3, 5 -guanosine-proflavine hydrate [358] and the spine of hydration in the minor groove of a 5-type oligodeoxynucleotide duplex [359]. They resulted in partial agreement and demonstrated the sensitivity of the method to the pair potentials used. 

In the minor groove of the B-DNA dodecamer d(CGCGAATTCGCG), such hydrogen bonding to 0(40 is a characteristic feature of the spine of hydration discussed below. 

A spine of hydration in the minor groove of B-DNA has been found in the central AATT sequence of the dodecamer d(CGCGAATTCGCG) [867]. As illustrated in Fig. 24.7 and in Fig. 24.9 b, water molecules span 0(2) and N(3) atoms of bases in adjacent base pairs, i.e., 0(2) Ow N(3), with additional close contacts to 0(4 ) atoms. These water molecules form the first hydration layer. They are connected by water molecules in the second layer such that each of the water molecules in the first layer is tetrahedrally coordinated. Because the N(2) amino groups in G/C sequences would interfere sterically with this regular spine of hydration , it is disrupted at both ends of the central AATT sequence in the dodecanucleotide. 

The minor groove of Z-DNA binds a spine of hydration. The water molecules are primarily hydrogen-bonded to the 0(2) atoms of the cytosine bases. These are cross-linked 0(2) W -0(2), and there are additional water molecules bridging these waters with phosphate oxygen atoms and with the guanine N(2) amino group (see Fig. 24.8 and 24.9 c). 

Because the spine of hydration in Z-DNA is so well defined and hydrogen-bonded to cytosine 0(2), guanine N(2), and phosphate oxygen atoms, we can... 

Fig. 24.8. Stereo diagram (side and top view) showing arrangement of spine of hydration in the minor groove of Z-DNA (see also Fig. 24.9 c, [876])...

The water pentagons in the major groove of A-DNA do not appear to have a significant influence on the stabilization of this DNA conformation. Otherwise, polymers with alternating A-T sequence such as poly(dA-dT) should occur preferentially in the A-form. Because this polymer favors the B-form, the spine of hydration is probably a stronger stabilizer of structure than the water pentagons. 

Subramanian S, Ravishanker G, Beveridge DL (1988) Theoretical considerations of the spine of hydration in the minor groove of d(CGCGAATTCGCG) d(CGCGAATTCGCG) Monte Carlo computer simulation. Proc Natl Acad Sci USA 85 1836-1840... 

The spine of hydration in the central AATT part of d(CGCGAATTC(jCG)2 is, perhaps, the most distinctive feature of the Dickerson-Drew B-DNA dodecamer (see Fig. 2)... 

Figure 2 Spacefill model of the Dickerson-Drew B-DNA dodecamer that illustrates the spine of hydration in the minor groove. The waters of minor groove hydration are shown in red (medium gray in black and white print), whereas the two DNA strands are shown in green (light gray in black and white print) and blue (dark gray in black and white print). The model was adapted from the high resolution X-ray data of Tereshko et al. (52).

Liepinsh E, Otting G, Wuthrich K. NMR observation of individual molecules of hydration water bound to DNA duplexes direct ev- 48. idence for a spine of hydration water present in aqueous solution. 

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