Drew-Dickerson dodecamer

NMR studies of water dynamics in the major groove of B-DNA are sparse. Although NOE cross-peaks between water and thymine methyl protons and guanine 8H and adenine 8H protons in the major groove of the Dickerson-Drew dodecamer have been identified, the estimated lifetimes on the order of 200 to 500 ps are short compared with that of water in the minor groove (26, 28). MRD measurements at 4 ° C have... 

Eigure 6. The G-N7 (a) and A-N6 and T-04 sites (b) in a typical B-DNA duplex (Dickerson-Drew dodecamer d(5 -CGCGAATTCGCG-3 )2, (PDB ID IBNA). The duplex in the right view has been rotated 180° with respect to the left view. (See color insert.)... 

Ikeda H, Fernandez R, WiUc A, Barchi JJ Jr, Huang X, Marquez VE (1998) The effect of two antipodal fluorine-induced sugar puckers on the conformation and stability of the Dickerson-Drew dodecamer duplex[d(CGCGAATTCGCG)]2. Nucleic Acids Res 26 2237-2244... 

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).

Tereshko V, Minasov G, Egli M. The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution. J. Am. Chem. Soc. 1999 121 470-471. 

Figure 8 (Chapter 8). (a) The 6-bp PNA duplex based on the H2N-CGTACG-H strand (PDB IPUP), and (b) the 6-bp central fragment d(GAATTC)2 of the Dickerson-Drew DNA dodecamer (PDB IBNA).

Sodium ions have been proposed to bind to N3 of guanine or adenine and the 02 of cytosine or thymine in the minor groove of the DNA dodeeamer referred to as the Dickerson-Drew-B-DNA dodecamer. This sequence, the subjeet of several X-ray erystal structures extending to sub-Angstrom resolution, eontains a run of A T base pairs known as an A-tract. All monovalent cation sites are only partially oceupied in these struetures. Beeause sodium ions are diffieult to distinguish from water molecules using erystallographie teehniques, a bond-valence sum approaeh was employed in the analysis by Williams and eo-workers, who proposed that the DNA minor... 

Like and presumably Na, Rb ions bind to the central ApT step in the minor groove of the Dickerson-Drew-B-DNA dodecamer. The Rb site is partially occupied, and has a coordination sphere that consists of seven oxygen atoms, with four DNA-derived ligands and three aqua ligands. The ion is coordinated to the 0(2 atoms of two thymines and to two 04 sugar positions with distances ranging from 2.8 A to 3.5 A. 

Kopka ML, Fratini AV, Drew HR, Dickerson RE (1983) Ordered water structure around a B-DNA dodecamer. A quantitative study. J Mol Biol 163 129-146... 

Crystallographic study of mismatches have concentrated on sequences known to crystallise into which the mispairs were engineered. A common framework has been the B-DNA Drew-Dickerson dodecamer duplex, d(CGCGAATTCGCG) (19). Other templates have been A-form DNA octamers and Z-form hexamers (20). In each case a duplex containing two mispairs has been formed. This approach maximises the chances of getting well ordered single crystals and means that there is a native Watson-Crick structure for comparative purposes. 

Analysis of only selected parts of the system during the validation phase of research is a dangerous exercise and can lead to erroneous conclusions. We illustrate this by means of results from an unpublished 500 ps simulation on the Drew—Dickerson dodecamer sequence in its canonical form, surrounded by 2000 SPG waters in a hexagonal box. In this simulation, each counterion was associated with a phosphate group to form a neutral charge group and was restrained by a hemiharmonic potential centered at 6 A with a force constant of... 

Dickerson, R. E., 8c Drew, H. R. (1981). Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. Journal of Molecular Biology, 15,761. 

---