Results 51 to 60 of about 2,257,590 (274)

DNA topology and topoisomerases [PDF]

Biochemistry and Molecular Biology Education, 2009
AbstractDNA is essentially an extremely long double‐stranded rope in which the two strands are wound about one another. As a result, topological properties of the genetic material, including DNA underwinding and overwinding, knotting, and tangling profoundly influence virtually every major nucleic acid process.
Joseph E, Deweese, Michael A, Osheroff, Neil, Osheroff   +2 more
openaire   +2 more sources

TEX264 coordinates p97- and SPRTN-mediated resolution of topoisomerase 1-DNA adducts

Nature Communications, 2020
Eukaryotic topoisomerase 1 (TOP1) regulates DNA topology to ensure efficient DNA replication and transcription. Here, the authors reveal insights into the molecular resolution of topoisomerase 1-DNA adducts by TEX264, p97 and SPRTN.
John Fielden, Katherine Wiseman, Ignacio Torrecilla, Shudong Li, Samuel Hume, Shih-Chieh Chiang, Annamaria Ruggiano, Abhay Narayan Singh, Raimundo Freire, Sylvana Hassanieh, Enric Domingo, Iolanda Vendrell, Roman Fischer, Benedikt M. Kessler, Timothy S. Maughan, Sherif F. El-Khamisy, Kristijan Ramadan   +16 more
doaj   +1 more source

Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes. [PDF]

, 2015
Cations are known to mediate diverse interactions in nucleic acids duplexes but they are critical in the arrangement of four-stranded structures. Here, we use all-atom molecular dynamics simulations with explicit solvent to analyse the mechanical ...
Bergues-Pupo, AE, Fiasconaro A., Ana Elisa Bergues-pupo, Bergues-Pupo, A.E., Arias-Gonzalez, J. R., Morón, M.C., Fiasconaro, A., Bergues Pupo, Ana Elisa, Arias-Gonzalez, J. Ricardo, Arias-Gonzalez, J., Fiasconaro, Alessandro, Bergues-Pupo, A., Falo, Fernando, Morón, MC, Fiasconaro, A, Bergues-Pupo A.E., Morón, M. Carmen, Falo, F, J. Ricardo Arias-gonzalez, Ro Fiasconaro, Morón M.C., Falo, F., Arias-Gonzalez, JR, Falo F., Arias-Gonzalez J.R., O Falo   +25 more
core   +1 more source

The topology of the kinetoplast DNA network

Cell, 1995
Kinetoplast DNA (kDNA) of trypanosomatid parasites is a network of approximately 5000 catenated DNA minicircles and approximately 25 maxicircles. We developed the following strategy to deduce the topological linkage of the minicircles of the Crithidia fasciculata network.
Chen, Junghuei, Rauch, Carol A, White, James H, Englund, Paul T, Cozzarelli, Nicholas R   +4 more
openaire   +2 more sources

Beyond Node Degree: Evaluating AS Topology Models [PDF]

, 2012
This is the accepted version of 'Beyond Node Degree: Evaluating AS Topology Models', archived originally at arXiv:0807.2023v1 [cs.NI] 13 July 2008.Many models have been proposed to generate Internet Autonomous System (AS) topologies, most of which make ...
Mortier, R, Fay, D, Haddadi, H, Uhlig, S, Rio, M, Jamakovic, A, Maennel, O, Moore, AW   +7 more
core   +2 more sources

Topology‐Driven X‐Shaped DNA as a cGAS Stimulator to Promote Dendritic Cell Activation and Antitumor Vaccine Efficacy [PDF]

Advanced Science, EarlyView.
X‐shaped DNA promotes multivalent cGAS assembly and enhances cGAS‐STING signaling. When conjugated with antigenic peptides, the resulting X‐DNA‐based peptide vaccine promotes dendritic cell activation, antigen presentation, and antitumor T‐cell responses.
Jiabei Li, Xuan Wang, Dali Wei, Zhejie Chen, Ziyi Wang, Qing Yu, Yu Yang, Shengpeng Wang   +7 more
wiley   +2 more sources

Nucleosomal DNA has topological memory

Nature Communications
One elusive aspect of the chromosome architecture is how it constrains the DNA topology. Nucleosomes stabilise negative DNA supercoils by restraining a DNA linking number difference (∆Lk) of about −1.26.
Joana Segura, Ofelia Díaz-Ingelmo, Belén Martínez-García, Alba Ayats-Fraile, Christoforos Nikolaou, Joaquim Roca   +5 more
doaj   +1 more source

Investigating transcription factor dynamics in health and disease using FRAP

FEBS Letters, EarlyView.
FRAP analysis of GFP‐tagged transcription factors reveals how molecular mobility and target engagement change in response to drug treatment. By combining live‐cell imaging, quantitative model fitting, and statistical analysis, this approach uncovers transcription factor dynamics linked to disease mechanisms, providing a powerful framework for ...
Kannan Govindaraj, Carolina Vazquez Garzon, Jose Joaquin Velasco, Janine N. Post   +3 more
wiley   +1 more source

Changes in the Topology of DNA Replication Intermediates: In vivo vs In vitro [PDF]

, 2021
Most of the methods used to analyze DNA, including electrophoresis, electron microscopy or atomic force microscopy, involve de-proteinization, and it is well known that the removal of proteins affects DNA topology.
Schvartzman, Jorge Bernardo, Fernández Nestosa, María José, Martínez, Víctor, Hernández, Pablo, Krimer, Dora B.   +4 more
core  

Conserved binding mode but diverse interfaces of MreC‐PBP2 interactions

FEBS Letters, EarlyView.
The crystal structure of abMreC reveals a conserved two β‐barrel architecture and provides structural insights into its role within the bacterial elongasome. The abMreC–abPBP2 complex model identifies the molecular basis of MreC‐mediated PBP2 recognition, contributing to the regulation of peptidoglycan synthesis.
Hyunseok Jang, Hyo Been Jin, Chang Min Kim, So Yeon Lee, Hyun Ho Park   +4 more
wiley   +1 more source