Ordered water structure around a B-DNA dodecamer

Kopka, Mary L.; Fratini, Albert; Drew, Horace R.; Dickerson, Richard E.

doi:10.1016/0022-2836(83)90033-5

Cited by 478 publications

(266 citation statements)

References 16 publications

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“…This is a weak observation, but is worth putting on record because it is so intuitively reasonable. The major groove is large and free of ordered hydration structure, aside from a monolayer of water molecules associated with the polar N and O atoms of base edges (17,22). In contrast, the minor groove is narrower, and occupied by the zig-zag spine of hydration that is believed to stabilize the B conformation.…”

Section: +#4+4mentioning

confidence: 96%

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A random-walk model for helix bending in B-DNA.

Dickerson¹,

Kopka²,

Pjura³

1983

Proc. Natl. Acad. Sci. U.S.A.

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The double-helical B-DNA dodecamer of sequence d(C-G-C-G-A-A-T-T-C-G-C-G) has been refined independently from x-ray crystal structure analyses in five different variants: d(C-G-C-G-A-A-T-T-C-G-C-G) at 16 K, at room temperature, and with bound cis-diamminedichloroplatinum(II), and d(C-G-C-G-A-A-T-T-brC-G-C-G) in 60% 2-methyl-2,4-pentanediol at 20 degrees C and 7 degrees C. These helices display overall axial bends of 22 degrees, 18 degrees, 17 degrees, 14 degrees, and 3 degrees, respectively, providing an opportunity to investigate the nature of the bending process in B-DNA. Bending from one base pair to the next is best described as a stochastic or random-walk process, having forward, retrograde, and sidewise individual steps, but with an overall sense of bending. Individual steps almost always involve rolling of adjacent base pairs over one another along their long axes, not a tilting or wedge displacement that lifts neighboring base pairs apart at one end. A slight preference is observed for bending the double helix in a direction that compresses the major groove rather than the minor, and this is intuitively reasonable in view of the narrowness of the minor groove and its occupation by the spine of hydration that stabilizes the B form of DNA. This model predicts that, when DNA is wound around the nucleosome core, it should not be smoothly curved but should exhibit discrete bends every five base pairs as proposed by Zhurkin et al. [Zhurkin, V.B., Lysov, Y. P. & Ivanov, V. I. (1979) Nucleic Acids Res. 6, 1081-1096)]. Sharper bends may occur at alternate positions, where the major groove faces the nucleosome core.

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Section: +#4+4mentioning

confidence: 96%

“…2 (13,(21)(22)(23)(24). Crossed spheres in the major groove ofc are platinum, and large spheres in the major groove of d and e are bromines.…”

Section: Helices With Various Degrees Of Bendingmentioning

confidence: 99%

A random-walk model for helix bending in B-DNA.

Dickerson¹,

Kopka²,

Pjura³

1983

Proc. Natl. Acad. Sci. U.S.A.

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“…51,52 The presence of a spine of well-ordered water molecules in the minor groove of AT-rich DNA sequences has been derived from high-resolution X-ray crystallography and neutron diffraction studies. 36,53-55 The minor groove is unusually narrow in AT stretches and a primary shell of water molecules runs across the groove, bridging acceptor sites on adjacent AT/TA base pairs ( Figure 6).…”

Section: Hydration Of the Dna Groovesmentioning

confidence: 99%

What Drives Proteins into the Major or Minor Grooves of DNA?

Privalov

Dragan

Crane‐Robinson

et al. 2007

Journal of Molecular Biology

168

158

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The energetic profiles of a significant number of protein-DNA systems at 20°C reveal that, despite comparable Gibbs free energies, association with the major groove is primarily an enthalpy driven process, whereas binding to the minor groove is characterized by an unfavorable enthalpy that is compensated by favorable entropic contributions. These distinct energetic signatures for major versus minor groove binding are irrespective of the magnitude of DNA bending and/or the extent of binding-induced protein refolding. The primary determinants of their different energetic profiles appear to be the distinct hydration properties of the major and minor grooves, namely that the water in the AT-rich minor groove is in a highly ordered state and its removal results in a substantial positive contribution to the binding entropy. Since the entropic forces driving protein binding into the minor groove are a consequence of displacing water ordered by the regular arrangement of polar contacts, they cannot be regarded as hydrophobic. KeywordsDNA binding; DNA grooves; hydration; thermodynamics; electrostatics Structural and energetic characterizations of protein-nucleic acid complexes are important for a better understanding of the molecular interactions that govern transcriptional regulation. Of particular importance are the energetic profiles of DNA binding domains (DBDs) interacting with their target recognition sites. DBDs are known to interact specifically with either the major or minor grooves of DNA, with binding-induced structural effects ranging from negligible perturbation of the B-DNA conformation to substantial distortions, such as bending and kinking. One can then ask if there are qualitative differences in the forces driving protein binding to the different grooves of DNA. Comparing the association constants of these two types of DBDs does not furnish a satisfactory answer, since both categories contain examples of stronger and weaker binding interactions. An answer to this question therefore requires a detailed analysis of the forces involved in the formation of the specific protein-DNA complexes. This assumes not only measurement of the association constant but also determination of the Gibbs energy and its enthalpic and entropic components over a broad range of conditions, particularly temperature and ionic strength. In this review, we analyze the thermodynamic characteristics of protein binding to DNA published over the last several years. This overall consideration has revealed qualitative differences in the energetic signatures of

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“…7 shows a plot of the minor groove width for the yoxapentamidine -dodecamer complex, together with the native structure and those for complexes with the closely related bis(amidine) ligands pentamidine and propamidine bound to this dodecamer. It can be seen that the native DNA, which has the minor groove filled by a spine of hydration (Kopka et al, 1983), has a narrow groove compared with the three ligand-bound complexes. We note that the y-oxapen-P-P pair tamidine structure has its smallest groove width in the vicinity of the 9-20 residue separation.…”

Section: Influence Of Y-oxapentamidine On Dna Conformationmentioning

confidence: 99%

Crystal Structure of γ‐Oxapentamidine Complexed with d(CGCGAATTCGCG)₂

Nunn

Jenkins

Neidle

1994

European Journal of Biochemistry

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The crystal structure of the complex of γ‐oxapentamidine and the DNA dodecamer d(CGCGAATTCGCG)2 has been determined to a resolution of 0.22 nm and an R factor of 18.9%. The γ‐oxapentamidine ligand interacts with the dodecamer by classic minor groove binding via interactions within the Arich region of the minor groove. A chain of solvent molecules lies along the mouth of the minor groove on the outside of the bound ligand. The structural details of the complex are discussed and compared with the closely analogous complex with pentamidine bound to the same dodecamer [Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104–7109]. The amidinium groups of the ligand do not hydrogen bond to bases, but are in close contact with O4′ sugar ring atoms. This in part explains the reduced DNA binding affinity of this ligand compared to pentamidine.

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Ordered water structure around a B-DNA dodecamer

Cited by 478 publications

References 16 publications

A random-walk model for helix bending in B-DNA.

A random-walk model for helix bending in B-DNA.

What Drives Proteins into the Major or Minor Grooves of DNA?

Crystal Structure of γ‐Oxapentamidine Complexed with d(CGCGAATTCGCG)₂

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Ordered water structure around a B-DNA dodecamer

Cited by 478 publications

References 16 publications

A random-walk model for helix bending in B-DNA.

A random-walk model for helix bending in B-DNA.

What Drives Proteins into the Major or Minor Grooves of DNA?

Crystal Structure of γ‐Oxapentamidine Complexed with d(CGCGAATTCGCG)2

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Crystal Structure of γ‐Oxapentamidine Complexed with d(CGCGAATTCGCG)₂