Structure of a dimer of the Sulfolobus solfataricus MCM N-terminal domain reveals a potential role in MCM ring opening

2021 ◽  
Vol 77 (6) ◽  
Author(s):  
Martin Meagher ◽  
Madison N. Spence ◽  
Eric J. Enemark
Keyword(s):  
Dna Replication ◽  
Double Helix ◽  
Sulfolobus Solfataricus ◽  
Replication Initiation ◽  
Terminal Domain ◽  
Closed Ring ◽  
Dna Strands ◽  
Ring Structures ◽  
Dna Strand ◽  
Dna Double Helix

Cells strongly regulate DNA replication to ensure genomic stability and prevent several diseases, including cancers. Eukaryotes and archaea strictly control DNA-replication initiation by the regulated loading of hexameric minichromosome maintenance (MCM) rings to encircle both strands of the DNA double helix followed by regulated activation of the loaded rings such that they then encircle one DNA strand while excluding the other. Both steps involve an open/closed ring transformation, allowing DNA strands to enter or exit. Here, the crystal structure of a dimer of the N-terminal domain of Sulfolobus solfataricus MCM with an intersubunit interface that is more extensive than in closed-ring structures, while including common interactions to enable facile interconversion, is presented. It is shown that the identified interface could stabilize open MCM rings by compensating for lost interactions at an open neighbor interface and that the prior open-ring cryo-EM structure of MCM loading has a similar extended interface adjacent to its open interface.

Structure of DNA and Nucleosome Observed by Ultrahigh-Resolution SEM

1990 ◽  
Vol 48 (3) ◽  
pp. 124-125
Author(s):  
Sumire Inaga ◽  
Hitoshi Osatake ◽  
Akihiro lino ◽  
Keiichi Tanaka
Keyword(s):  
Electron Microscopy ◽  
Double Helix ◽  
Replica Method ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Ultrahigh Resolution ◽  
Naked Dna ◽  
Dna Strands ◽  
Dna Strand ◽  
Dna Double Helix

So far, the ultrastructure of DNA strand and nucleosome had been observed mainly by transmission electron microscopy with some techniques (thin-sectioning, spreading method, replica method and so on). Among them, the freeze-etching replica method gave high magnified images of DNA double helix (Ruben et al., 1989). Further, scanning tunneling microscopy also elucidated the images of major and minor grooves in a helical DNA duplex. Though scanning electron microscopy (SEM) was also applied for observing chromatin structures, it had been difficult to observe clearly such small materials. Because, the resolution of SEM was too poor to investigate such fine structures. The obstruction of resolution, however, was overcome by the development of an ultrahigh resolution SEM (UHS-T1, Tanaka et al., 1985). Using the SEM, we could successfully observed naked DNA strands and nucleosomes of chicken erythrocyte nuclei without any metal-coating.Preparations were made by the microspreading procedure basically according to the method of Seki et al.

scholarly journals 3′ → 5′ Exonucleases of DNA Polymerases ϵ and δ Correct Base Analog Induced DNA Replication Errors on Opposite DNA Strands in Saccharomyces cerevisiae

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 717-726 ◽  
Author(s):  
Polina V Shcherbakova ◽  
Youri I Pavlov
Keyword(s):  
Dna Replication ◽  
Dna Polymerases ◽  
Replication Errors ◽  
Dna Strands ◽  
Base Analog ◽  
Chromosome Iii ◽  
Dna Strand ◽  
Dna Replication Errors ◽  
Yeast Mutants ◽  
Lagging Strand

Abstract The base analog 6-N-hydroxylaminopurine (HAP) induces bidirectional GC → AT and AT → GC transitions that are enhanced in DNA polymerase ϵ and δ 3′ → 5′ exonuclease-deficient yeast mutants, pol2-4 and pol3-01, respectively. We have constructed a set of isogenic strains to determine whether the DNA polymerases δ and ϵ contribute equally to proofreading of replication errors provoked by HAP during leading and lagging strand DNA synthesis. Site-specific GC → AT and AT → GC transitions in a Pol→, pol2-4 or pol3-01 genetic background were scored as reversions of ura3 missense alleles. At each site, reversion was increased in only one proofreading-deficient mutant, either pol2-4 or pol3-01, depending on the DNA strand in which HAP incorporation presumably occurred. Measurement of the HAP-induced reversion frequency of the ura3 alleles placed into chromosome III near to the defined active replication origin ARS306 in two orientations indicated that DNA polymerases ϵ and δ correct HAP-induced DNA replication errors on opposite DNA strands.

Mercury Electrodes in Nucleic Acid Electrochemistry: Sensitive Analytical Tools and Probes of DNA Structure. A Review

2004 ◽  
Vol 69 (4) ◽  
pp. 715-747 ◽  
Author(s):  
Miroslav Fojta
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Double Helix ◽  
Dna Structure ◽  
Electrochemical Analysis ◽  
Label Free ◽  
Helix Formation ◽  
Mercury Electrodes ◽  
Dna Strand ◽  
Dna Double Helix

This review is devoted to applications of mercury electrodes in the electrochemical analysis of nucleic acids and in studies of DNA structure and interactions. At the mercury electrodes, nucleic acids yield faradaic signals due to redox processes involving adenine, cytosine and guanine residues, and tensammetric signals due to adsorption/desorption of polynucleotide chains at the electrode surface. Some of these signals are highly sensitive to DNA structure, providing information about conformation changes of the DNA double helix, formation of DNA strand breaks as well as covalent or non-covalent DNA interactions with small molecules (including genotoxic agents, drugs, etc.). Measurements at mercury electrodes allow for determination of small quantities of unmodified or electrochemically labeled nucleic acids. DNA-modified mercury electrodes have been used as biodetectors for DNA damaging agents or as detection electrodes in DNA hybridization assays. Mercury film and solid amalgam electrodes possess similar features in the nucleic acid analysis to mercury drop electrodes. On the contrary, intrinsic (label-free) DNA electrochemical responses at other (non-mercury) solid electrodes cannot provide information about small changes of the DNA structure. A review with 188 references.

Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination

2003 ◽  
Vol 36 (4) ◽  
pp. 429-453 ◽  
Author(s):  
Chantal Prévost ◽  
Masayuki Takahashi
Keyword(s):  
Homologous Recombination ◽  
Structural Information ◽  
Double Helix ◽  
Genetic Material ◽  
Strand Exchange ◽  
Double Stranded Dna ◽  
Dna Deformation ◽  
Architectural Proteins ◽  
Dna Strands ◽  
Dna Strand

1. Introduction 4302. Transformations of the RecA filament 4312.1 The different forms of the RecA filament 4312.2 Orientation and position of the RecA monomers in the active filament 4332.3 Transmission of structural information along the filament 4333. RecA-induced DNA deformations 4353.1 Characteristics of RecA-bound DNA 4353.2 Stretching properties of double-stranded DNA 4363.3 DNA bound to architectural proteins 4373.4 Implications for RecA-induced DNA deformations 4383.5 Axial distribution of the DNA stretching deformation 4384. Contacts between RecA and the DNA strands 4404.1 The DNA-binding sites 4404.2 Possible arrangement of loops L1 and L2 and the three bound strands of DNA 4425. Strand arrangement during pairing reorganization 4445.1 Hypotheses for DNA strand association 4445.2 Association via major or minor grooves 4465.3 Post-strand exchange geometries 4466. Conclusion 4477. Acknowledgments 4488. References 448Homologous recombination consists of exchanging DNA strands of identical or almost identical sequence. This process is important for both DNA repair and DNA segregation. In prokaryotes, it involves the formation of long helical filaments of the RecA protein on DNA. These filaments incorporate double-stranded DNA from the cell's genetic material, recognize sequence homology and promote strand exchange between the two DNA segments. DNA processing by these nucleofilaments is characterized by large amplitude deformations of the double helix, which is stretched by 50% and unwound by 40% with respect to B-DNA. In this article, information concerning the structure and interactions of the RecA, DNA and ATP molecules involved in DNA strand exchange is gathered and analyzed to present a view of their possible arrangement within the filament, their behavior during strand exchange and during ATP hydrolysis, the mechanism of RecA-promoted DNA deformation and the role of DNA deformation in the process of homologous recombination. In particular, the unusual characteristics of DNA within the RecA filament are compared to the DNA deformations locally induced by architectural proteins which bind in the DNA minor groove. The possible role and location of two flexible loops of RecA are discussed.

scholarly journals Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

2014 ◽  
Vol 10 ◽  
pp. 1589-1595 ◽  
Author(s):  
Christian B Winiger ◽  
Simon M Langenegger ◽  
Oleg Khorev ◽  
Robert Häner
Keyword(s):  
Double Helix ◽  
Building Blocks ◽  
Supramolecular Interactions ◽  
Stacking Interactions ◽  
Average Value ◽  
Π Stacking ◽  
Dna Strands ◽  
Polycyclic Aromatic ◽  
The Stability ◽  
Dna Double Helix

Aromatic π–π stacking interactions are ubiquitous in nature, medicinal chemistry and materials sciences. They play a crucial role in the stacking of nucleobases, thus stabilising the DNA double helix. The following paper describes a series of chimeric DNA–polycyclic aromatic hydrocarbon (PAH) hybrids. The PAH building blocks are electron-rich pyrene and electron-poor perylenediimide (PDI), and were incorporated into complementary DNA strands. The hybrids contain different numbers of pyrene–PDI interactions that were found to directly influence duplex stability. As the pyrene–PDI ratio approaches 1:1, the stability of the duplexes increases with an average value of 7.5 °C per pyrene–PDI supramolecular interaction indicating the importance of electrostatic complementarity for aromatic π–π stacking interactions.

Symmetry-adapted digital modeling II. The double-helix B-DNA

2016 ◽  
Vol 72 (3) ◽  
pp. 312-323 ◽  
Author(s):  
A. Janner
Keyword(s):  
Dimensional Space ◽  
Double Helix ◽  
Three Dimensional ◽  
Reduction Factor ◽  
Lattice Points ◽  
Three Dimensions ◽  
Coarse Grained ◽  
Digital Modeling ◽  
Dna Strands ◽  
Dna Double Helix

The positions of phosphorus in B-DNA have the remarkable property of occurring (in axial projection) at well defined points in the three-dimensional space of a projected five-dimensional decagonal lattice, subdividing according to the golden mean ratio τ:1:τ [with τ = (1+\sqrt {5})/2] the edges of an enclosing decagon. The corresponding planar integral indicesn1,n2,n3,n4(which are lattice point coordinates) are extended to include the axial indexn5as well, defined for each P position of the double helix with respect to the single decagonal lattice ΛP(aP,cP) withaP= 2.222 Å andcP= 0.676 Å. A finer decagonal lattice Λ(a,c), witha=aP/6 andc=cP, together with a selection of lattice points for each nucleotide with a given indexed P position (so as to define a discrete set in three dimensions) permits the indexing of the atomic positions of the B-DNA d(AGTCAGTCAG) derived by M. J. P. van Dongen. This is done for both DNA strands and the single lattice Λ. Considered first is the sugar–phosphate subsystem, and then each nucleobase guanine, adenine, cytosine and thymine. One gets in this way a digital modeling of d(AGTCAGTCAG) in a one-to-one correspondence between atomic and indexed positions and a maximal deviation of about 0.6 Å (for the value of the lattice parameters given above). It is shown how to get a digital modeling of the B-DNA double helix for any given code. Finally, a short discussion indicates how this procedure can be extended to derive coarse-grained B-DNA models. An example is given with a reduction factor of about 2 in the number of atomic positions. A few remarks about the wider interest of this investigation and possible future developments conclude the paper.

scholarly journals Mechanism of RPA-Facilitated Processive DNA Unwinding by the Eukaryotic CMG Helicase

2019 ◽  
Author(s):  
Hazal B. Kose ◽  
Sherry Xie ◽  
George Cameron ◽  
Melania S. Strycharska ◽  
Hasan Yardimci
Keyword(s):  
Single Molecule ◽  
Replication Fork ◽  
Double Helix ◽  
Dna Unwinding ◽  
Helicase Activity ◽  
Replicative Helicase ◽  
Double Stranded Dna ◽  
Order Of Magnitude ◽  
Dna Strand ◽  
Dna Double Helix

AbstractThe DNA double helix is unwound by the Cdc45/Mcm2-7/GINS (CMG) complex at the eukaryotic replication fork. While isolated CMG unwinds duplex DNA very slowly, its fork unwinding rate is stimulated by an order of magnitude by single-stranded DNA binding protein, RPA. However, the molecular mechanism by which RPA enhances CMG helicase activity remained elusive. Here, we demonstrate that engagement of CMG with parental double-stranded DNA (dsDNA) at the replication fork impairs its helicase activity, explaining the slow DNA unwinding by isolated CMG. Using single-molecule and ensemble biochemistry, we show that binding of RPA to the excluded DNA strand prevents duplex engagement by the helicase and speeds up CMG-mediated DNA unwinding. When stalled due to dsDNA interaction, DNA rezipping-induced helicase backtracking re-establishes productive helicase-fork engagement underscoring the significance of plasticity in helicase action. Together, our results elucidate the dynamics of CMG at the replication fork and reveal how other replisome components can mediate proper DNA engagement by the replicative helicase to achieve efficient fork progression.

scholarly journals Inhibition of Human Chk1 Causes Increased Initiation of DNA Replication, Phosphorylation of ATR Targets, and DNA Breakage

2005 ◽  
Vol 25 (9) ◽  
pp. 3553-3562 ◽  
Author(s):  
Randi G. Syljuåsen ◽  
Claus Storgaard Sørensen ◽  
Lasse Tengbjerg Hansen ◽  
Kasper Fugger ◽  
Cecilia Lundin ◽  
...  
Keyword(s):  
Dna Replication ◽  
Genome Stability ◽  
Protein A ◽  
S Phase ◽  
Replication Initiation ◽  
Dna Breakage ◽  
Histone H2ax ◽  
Initiation Of Dna Replication ◽  
Dna Strand ◽  
Interfering Rna

ABSTRACT Human checkpoint kinase 1 (Chk1) is an essential kinase required to preserve genome stability. Here, we show that Chk1 inhibition by two distinct drugs, UCN-01 and CEP-3891, or by Chk1 small interfering RNA (siRNA) leads to phosphorylation of ATR targets. Chk1-inhibition triggered rapid, pan-nuclear phosphorylation of histone H2AX, p53, Smc1, replication protein A, and Chk1 itself in human S-phase cells. These phosphorylations were inhibited by ATR siRNA and caffeine, but they occurred independently of ATM. Chk1 inhibition also caused an increased initiation of DNA replication, which was accompanied by increased amounts of nonextractable RPA protein, formation of single-stranded DNA, and induction of DNA strand breaks. Moreover, these responses were prevented by siRNA-mediated downregulation of Cdk2 or the replication initiation protein Cdc45, or by addition of the CDK inhibitor roscovitine. We propose that Chk1 is required during normal S phase to avoid aberrantly increased initiation of DNA replication, thereby protecting against DNA breakage. These results may help explain why Chk1 is an essential kinase and should be taken into account when drugs to inhibit this kinase are considered for use in cancer treatment.

Stereoscopic Visualization of Spermidine-DNA Torus Structure Prepared by the Freeze-Fracture, Deep-Etch Technique

1981 ◽  
Vol 39 ◽  
pp. 438-439
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx ◽  
Thomas C. Reynolds
Keyword(s):  
Double Helix ◽  
Freeze Fracture ◽  
Etching Technique ◽  
Calf Thymus ◽  
Quick Freezing ◽  
Metal Levels ◽  
Dna Strands ◽  
Dna Double Helix ◽  
Stereoscopic Visualization ◽  
Condensed Dna

Freeze-fracture TEM has been used to visualize spermidine-DNA complexes╌a model system for bacteriophage DNA packaging. We have observed the toroidal shape and bacteriophage size (770Å) of spermidine-condensed DNA particles prepared by quick freezing of DNA-spermidine solutions followed by a freeze-fracture, deep-etching technique. Single direction shadowing with low Pt-C metal levels (9Å thick) has allowed us to demonstrate that the freeze-fracture technique is capable of revealing the organization of separate double helical DNA strands on the torus surface. The spermidine-DNA toruses exhibited surface Pt-C decoration consistent with the DNA double helix being circumferentially wrapped to form the torus. In addition, we have demonstrated that a hydrated sample shows the same toroidal shapes that have been previously demonstrated by Chattoraj et. al, in a dehydrated preparation.We performed freeze-fracture TEM studies of spermidine condensed (0.2 mM) Calf Thymus DNA (5 μg/ml) complexes in 1 mM NaCl, 10 mM Tris pH 7.0. Samples were freeze-fractured and etched for 13 min at -97°C.

RNA:DNA triple helices: from peculiar structures to pervasive chromatin regulators

2021 ◽  
Author(s):  
Andreas Adam Greifenstein ◽  
SoYoung Jo ◽  
Holger Bierhoff
Keyword(s):  
Protein Interactions ◽  
Current Knowledge ◽  
Double Helix ◽  
Wide Distribution ◽  
Detection Methods ◽  
Protein Coding ◽  
Functional Characterisation ◽  
Triple Helices ◽  
Dna Strand ◽  
Dna Double Helix

Abstract The genomes of complex eukaryotes largely contain non-protein-coding DNA, which is pervasively transcribed into a plethora of non-coding RNAs (ncRNAs). The functional importance of many of these ncRNAs has been investigated in the last two decades, revealing their crucial and multifaceted roles in chromatin regulation. A common mode of action of ncRNAs is the recruitment of chromatin modifiers to specific regions in the genome. Whereas many ncRNA–protein interactions have been characterised in detail, binding of ncRNAs to their DNA target sites is much less understood. Recently developed RNA-centric methods have mapped the genome-wide distribution of ncRNAs, however, how ncRNAs achieve locus-specificity remains mainly unresolved. In terms of direct RNA–DNA interactions, two kinds of triple-stranded structures can be formed: R-loops consisting of an RNA:DNA hybrid and a looped out DNA strand, and RNA:DNA triple helices (triplexes), in which the RNA binds to the major groove of the DNA double helix by sequence-specific Hoogsteen base pairing. In this essay, we will review the current knowledge about RNA:DNA triplexes, summarising triplex formation rules, detection methods, and ncRNAs reported to engage in triplexes. While the functional characterisation of RNA:DNA triplexes is still anecdotal, recent advances in high-throughput and computational analyses indicate their widespread distribution in the genome. Thus, we are witnessing a paradigm shift in the appreciation of RNA:DNA triplexes, away from exotic structures towards a prominent mode of ncRNA–chromatin interactions.

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