Groove hydration

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

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, Leupin W, Otting G. Hydration of DNA in aqueous solution NMR evidence for a kinetic destabilization of the minor 50. groove hydration of d(TTAA)2 versus d(AATT)2 segments. Nucl. 

Jacobson A, Leupin W, Liepinsh E, Otting F. Minor groove hydration of DNA in aqueous solution sequence-dependent next neighbor effect of the hydration lifetimes in d(TTAA)2 segments 52. measured by NMR spectroscopy. Nucl. Acids Res. 1996 24 2911-2918. 

Lan and McLaughlin have demonstrated that minor groove hydration is critical to the stability of DNA duplexes. By replacing dA with 3-deaza-dA, and T with 3-methyl-2-pyrimidione they demonstrated that the of dA and of T are involved with hydration in the minor groove, and using the analogues is destabilising in duplex DNA. 

V, P. Chuprina, U. Heinemann, A. A. Nurislamov, P. Zielenkiewicz, and R. E. Dickerson, Proc. Natl. Acad. Set. USA, 88, 593 (1991). Molecular Dynamics Simulation of the Hydration Shell of a B-DNA Decamer Reveals Two Main Types of Minor-Groove Hydration Depending on Groove Width. 

The NMR study by Wiithrich and coworkers has shown that there is a cavity between the protein and the DNA in the major groove of the Antennapedia complex. There are several water molecules in this cavity with a residence time with respect to exchange with bulk water in the millisecond to nanosecond range. These observations indicate that at least some of the specific protein-DNA interactions are short-lived and mediated by water molecules. In particular, the interactions between DNA and the highly conserved Gin 50 and the invariant Asn 51 are best rationalized as a fluctuating network of weak-bonding interactions involving interfacial hydration water molecules. 

Fig. 20. Schematic representation of the unrolled major groove of the MPD 7 helix showing the first hydration shell, consisting of all solvent molecules that are directly associated with base edge N and O atoms. Base atoms are labeled N4,04, N6,06 and N7 solvent peaks are numbered. Interatomic distances are given in Aup to 3,5 A represented by unbroken lines, between 3,5-4,1 A by dotted lines. The eight circles connected by double-lines represent the image of a spermine molecule bound to phosphate groups P2 and P22. There are 20 solvent molecules in a first hydration layer associated with N- and O-atoms l58)...

Fig. 21. Schematic representation of the second hydration shell in the major groove of MPD7 including all the water molecules interacting with those of the first shell (broken circles). Interacting phosphate groups are marked by numbered dots1581...

The three bidendate hydration mentioned above are all involved in hydration of the major groove, but only type 1 is encountered in the first shell hydration of the... 

Figure 21 shows the arrangement of the water molecules in the second hydration shell in the major groove of MPD 7. It contains all the water molecules associated with those of the primary layer indicated by broken circles, and those interacting with one another in a network. 

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). 

An analysis of the hydration structure of water molecules in the major and minor grooves in B-DNA has shown that there is a filament of water molecules connecting both the inter and the intra phosphate groups of the two strands of B-DNA. However, such a connectivity is absent in the case of Z-DNA confirming earlier MC simulation results. The probability density distributions of the counterions around DNA shows deep penetration of the counterions in Z-DNA compared to B-DNA. Further, these distributions suggest very limited mobility for the counterions and show well defined counter-ion pattern as originally suggested in the MC study. 

Fig. 7. Hydration of DNA, and with a drug recognized in the minor groove. Time scales are indicated for bulk water, dynamically ordered water, configurational changes and structured water...

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