scholarly journals Double-stranded DNA fragment shows a significant decrease in double-helix stability after binding of monofunctional platinum amine compounds

1989 ◽  
Vol 111 (11) ◽  
pp. 4123-4125 ◽  
Author(s):  
Carla J. Van Garderen ◽  
Leo P. A. Van Houte ◽  
Hans Van den Elst ◽  
Jacques H. Van Boom ◽  
Jan Reedijk
Keyword(s):  
Double Helix ◽  
Double Stranded Dna ◽  
Helix Stability ◽  
Dna Fragment ◽  
Amine Compounds

scholarly journals Heterogeneous nuclear ribonucleoprotein D0B is a sequence-specificDNA-binding protein

1999 ◽  
Vol 338 (2) ◽  
pp. 417-425 ◽  
Author(s):  
Mate TOLNAY ◽  
Lyudmila A. VERESHCHAGINA ◽  
George C. TSOKOS
Keyword(s):  
Dna Sequences ◽  
Rna Binding ◽  
Binding Protein ◽  
Double Helix ◽  
Physiological Role ◽  
Single Stranded Dna ◽  
Heterogeneous Nuclear Ribonucleoprotein ◽  
Double Stranded Dna ◽  
Nuclear Ribonucleoprotein

Complement receptor 2 (CR2) is important in the regulation of the B lymphocyte response; the regulation of its expression is therefore of central importance. We recently reported that a 42 kDa heterogeneous nuclear ribonucleoprotein (hnRNP) is involved in the transcriptional regulation of the human CR2 gene [Tolnay, Lambris and Tsokos (1997) J. Immunol. 159, 5492–5501]. We cloned the cDNA encoding this protein and found it to be identical with hnRNP D0B, a sequence-specific RNA-binding protein. By using a set of mutated oligonucleotides, we demonstrated that the recombinant hnRNP D0B displays sequence specificity for double-stranded oligonucleotide defined by the CR2 promoter. We conducted electrophoretic mobility-shift assays to estimate the apparent Kd of hnRNP D0B for the double-stranded DNA motif and found it to be 59 nM. Interestingly, hnRNP D0B displayed affinities of 28 and 18 nM for the sense and anti-sense strands of the CR2 promoter-defined oligonucleotide respectively. The significantly greater binding affinity of hnRNP D0B for single-stranded DNA than for double-stranded DNA suggests that the protein might melt the double helix. The intranuclear concentration of sequence-specific protein was estimated to be 250–400 nM, indicating that the protein binds to the CR2 promoter in vivo. Co-precipitation of a complex formed in vivo between hnRNP D0B and the TATA-binding protein demonstrates that hnRNP D0B interacts with the basal transcription apparatus. Our results suggest a new physiological role for hnRNP D0B that involves binding to double- and single-stranded DNA sequences in a specific manner and functioning as a transcription factor.

scholarly journals Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA Fragment

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Zhuang Wang ◽  
Hao Fang ◽  
Se Wang ◽  
Fan Zhang ◽  
Degao Wang
Keyword(s):  
Carbon Nanotube ◽  
Quantum Dot ◽  
Molecular Interactions ◽  
Carbon Nanoparticles ◽  
Large Scale ◽  
Electrostatic Force ◽  
Md Simulations ◽  
Single Walled Carbon Nanotube ◽  
Double Stranded Dna ◽  
Dna Fragment

Molecular interactions between carbon nanoparticles (CNPs) and a double-stranded deoxyribonucleic acid (dsDNA) fragment were investigated using molecular dynamics (MD) simulations. Six types of CNPs including fullerenes (C60and C70), (8,0) single-walled carbon nanotube (SWNT), (8,0) double-walled carbon nanotube (DWNT), graphene quantum dot (GQD), and graphene oxide quantum dot (GOQD) were studied. Analysis of the best geometry indicates that the dsDNA fragment can bind to CNPs through pi-stacking and T-shape. Moreover, C60, DWNT, and GOQD bind to the dsDNA molecules at the minor groove of the nucleotide, and C70, SWNT, and GQD bind to the dsDNA molecules at the hydrophobic ends. Estimated interaction energy implies that van der Waals force may mainly contribute to the mechanisms for the dsDNA-C60, dsDNA-C70, and dsDNA-SWNT interactions and electrostatic force may contribute considerably to the dsDNA-DWNT, dsDNA-GQD, and dsDNA-GOQD interactions. On the basis of the results from large-scale MD simulations, it was found that the presence of the dsDNA enhances the dispersion of C60, C70, and SWNT in water and has a slight impact on DWNT, GQD, and GOQD.

scholarly journals Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix

2010 ◽  
Vol 21 (39) ◽  
pp. 395501 ◽  
Author(s):  
Utkur Mirsaidov ◽  
Jeffrey Comer ◽  
Valentin Dimitrov ◽  
Aleksei Aksimentiev ◽  
Gregory Timp
Keyword(s):  
Double Helix ◽  
Double Stranded Dna

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.

Na2CO3Influence on DNA Double Helix Stability: Strong Anion Destabilizing Effect

2003 ◽  
Vol 20 (6) ◽  
pp. 801-809 ◽  
Author(s):  
Elena N. Galyuk ◽  
Dmitri Y. Lando ◽  
Valentina P. Egorova ◽  
Hwa Dai ◽  
Yury M. Dosin
Keyword(s):  
Double Helix ◽  
Helix Stability ◽  
Dna Double Helix

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 On-Glass Optoelectronic Platform for On-Chip Detection of DNA

Proceedings ◽  
2018 ◽  
Vol 2 (13) ◽  
pp. 1014 ◽  
Author(s):  
Domenico Caputo ◽  
Francesca Costantini ◽  
Nicola Lovecchio ◽  
Marco Nardecchia ◽  
Augusto Nascetti ◽  
...  
Keyword(s):  
Spectral Properties ◽  
Double Helix ◽  
Lab On Chip ◽  
Double Stranded Dna ◽  
Waste Production ◽  
Interferential Filter ◽  
On Chip ◽  
High Fluorescence ◽  
Hydrogenated Amorphous ◽  
Fluorescent Molecules

Lab-on-chip are analytical systems which, compared to traditional methods, offer significant reduction of sample, reagent, energy consumption and waste production. Within this framework, we report on the development and testing of an optoelectronic platform suitable for the on-chip detection of fluorescent molecules. The platform combines on a single glass substrate hydrogenated amorphous silicon photosensors and a long pass interferential filter. The design of the optoelectronic components has been carried out taking into account the spectral properties of the selected fluorescent molecule. We have chosen the [Ru(phen)2(dppz)]2+ which exhibits a high fluorescence when it is complexed with nucleic acids in double helix. The on-glass optoelectronic platform, coupled with a microfluidic network, has been tested in detection of double-stranded DNA (dsDNA) reaching a detection limit as low as 10 ng/µL.

scholarly journals Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons

Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 241
Author(s):  
Enrique Maciá
Keyword(s):  
Base Pair ◽  
Double Helix ◽  
Three Dimensional ◽  
Dna Molecules ◽  
Analytical Treatment ◽  
Dynamical Equations ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Collective Oscillations ◽  
Triplet Codon

A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment that considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard–Dauxois–Bishop model, we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables corresponding to the bp local scale with those of the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.

Sign in / Sign up

Export Citation Format

Share Document