Crystal structure analysis of a complete turn of B-DNA

Wing, Richard M.; Drew, Horace R.; Takano, Tsunehiro; Broka, Chris A.; Tanaka, Shoji; Itakura, Keiichi; Dickerson, Richard E.

doi:10.1038/287755a0

Cited by 840 publications

(576 citation statements)

References 11 publications

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“…PCNA forms an 86-kDa homotrimeric ring 2 that encircles the DNA and anchors binding partners, preventing them from falling off the genomic template. The ring has an inner diameter of B35 Å, much wider than the B24 Å diameter of a DNA duplex in the B-form 3 . Apart from DNAediting factors, PCNA also interacts with non-enzymatic proteins that regulate cell cycle control and survival 4,5 .…”

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confidence: 99%

Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair

et al. 2015

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The intrinsically disordered protein p15 PAF regulates DNA replication and repair by binding to the proliferating cell nuclear antigen (PCNA) sliding clamp. We present the structure of the human p15 PAF -PCNA complex. Crystallography and NMR show the central PCNA-interacting protein motif (PIP-box) of p15 PAF tightly bound to the front-face of PCNA. In contrast to other PCNA-interacting proteins, p15 PAF also contacts the inside of, and passes through, the PCNA ring. The disordered p15 PAF termini emerge at opposite faces of the ring, but remain protected from 20S proteasomal degradation. Both free and PCNA-bound p15 PAF binds DNA mainly through its histone-like N-terminal tail, while PCNA does not, and a model of the ternary complex with DNA inside the PCNA ring is consistent with electron micrographs. We propose that p15 PAF acts as a flexible drag that regulates PCNA sliding along the DNA and facilitates the switch from replicative to translesion synthesis polymerase binding.

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confidence: 99%

Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair

et al. 2015

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“…A year later, the second structure 5 uncovered lefthanded DNA. It was only in 1980 that the right-handed double helix proposed in 1953 could be seen in atomic detail 6 .…”

Section: Dna Discoveries Through Crystallographymentioning

confidence: 98%

Why should we help politicians to wage war?

Amit

2003

Nature

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“…responding to an overall B-DNA structure, exhibits many local deviations from it [4,5]. Further, more direct evidence of a non-uniform backbone conformation of DNA has been obtained by 31P NMR spectroscopy [6] and there is also evidence for the possible coexistence of the A and B conformations along a synthetic nucleic acid duplex [7,8].…”

Section: (C-g-c-g-a-a-t-t-c-g-c-g) Which Although Cor-mentioning

confidence: 99%

Two Aspects of DNA Polymorphism and Microheterogeneity:

Pullman

Lavery

Pullman

1982

European Journal of Biochemistry

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Polymorphism and microheterogeneity of DNA appear today as being capable of having important biological consequences. This paper presents a synthetic view of two major properties of the main known forms of DNA (A, B, alternating B, C, D and Z), namely their molecular electrostatic potentials and stcric accessibilities.Variations in these properties are explained in terms of the conformational changes involved and deductions are drawn concerning their influence on the interactive properties of DNA with external agents.Since the early studies of D N A structure it has been recognized that this biopolymer may exist in different conformational forms, dependent on the external conditions to which it is exposed (humidity, salt concentration, etc.). These allomorphic forms are designated by the letters, A, B, C etc., the B form being currently considered as biologically the most significant.More recently it has become evident that conformational changes may also be induced by varying the sequence of the base pairs, a situation which necessarily leads to the consideration of a possible microheterogeneity of native DNA as a function of the order of the base pairs along its axis. Two recent works seem to have had a particularly strong influence in bringing this situation to light. One is the discovery of a family of left-handed DNA double helices, termed Z DNAs, found in the crystal of the self-complementary hexamer d(C-G-C-G-C-G) [1,2] and in the high salt solution of poly(dG-dC) . poly(dG-dC) [3]. The left-handedness, apparently characteristic of this sequence, as opposed to the usual right-handedness of DNAs, is a particularly impressive example of a sequence-dependent conformational change. The second discovery concerns the determination of the X-ray structure of the single crystal of the self-complementary dode- (C-G-C-G-A-A-T-T-C-G-C-G) which, although cor-responding to an overall B-DNA structure, exhibits many local deviations from it [4,5]. Further, more direct evidence of a non-uniform backbone conformation of DNA has been obtained by 31P NMR spectroscopy [6] and there is also evidence for the possible coexistence of the A and B conformations along a synthetic nucleic acid duplex [7,8].Such a heterogeneity of DNA is bound to have an important influence on its biochemical and, consequently, its biological behavior and, particularly, on the specificity of its interaction or association with external agents. In fact, it is known that, for example, the oligopeptide antibiotics netropsin and distamycin A have very different affinities for differently sequenced DNAs or for the different DNA conformers, A and B [9-111. Similarly, when the establishment of the Ahbreviutions. C8(G), C-8 of guanine, and similarly for the otherreactive atoms of the purines and pyrimidines. structure of Z D N A indicated that certain of its base-pair atoms on its convex face are unusually exposed, the hypothesis was put forward [1,2] that if Z-DNA segments were interspersed within a B-DNA chain, these atoms could represent privileged targets...

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Crystal structure analysis of a complete turn of B-DNA

Cited by 840 publications

References 11 publications

Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair

Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair

Why should we help politicians to wage war?

Two Aspects of DNA Polymorphism and Microheterogeneity:

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