Results 51 to 60 of about 124,583 (279)

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

Topology of Viral DNA

, 2010
Chromosome organization plays a key role in many biological processes. In viruses genome organization is essential for the packaging and releasing of the genome as well as for maintaining the stability of the viral capsid. This organization varies across different families and is highly dependent on the virus morphogenetic pathway (Casjens, 1997).
Arsuaga, Javier, Roca, Joaquim, Sumners, De Witt   +2 more
openaire   +2 more sources

The Topology of Scaffold Routings on Non-Spherical Mesh Wireframes [PDF]

, 2020
The routing of a DNA-origami scaffold strand is often modelled as an Eulerian circuit of an Eulerian graph in combinatorial models of DNA origami design.
Saito, Masahico, Mohammed, Abdulmelik, Jonoska, Nataša   +2 more
core   +1 more source

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

Phosphoinositides and inositol phosphates as molecular glues

FEBS Letters, EarlyView.
Inositol phosphates (IPs) and phosphoinositides (PIPs) regulate diverse eukaryotic processes. Beyond recruiting signaling proteins or acting as structural cofactors, recent studies suggest they mediate protein–protein interactions as natural molecular glues.
Aleshia Seaton‐Terry, Alexander J. Cutright, Mong Na Claire Loi, Jessica Martin, Joseph W. Gilligan, Jakub N. Kubina, Michael J. Arambula, Susanna Tanada Palmu, Daniella Zhou, Raymond D. Blind   +9 more
wiley   +1 more source

Facile Characterization of Topology of DNA Catenanes [PDF]

Biophysical Journal, 2020
During the preparation of single-stranded DNA catenanes, topological isomers of different linking numbers (Lk) are intrinsically produced, and they must be separated from each other to construct sophisticated nanostructures accurately. In many previous studies, however, mixtures of these isomers were directly employed to construct nanostructures ...
Lin, Li, Ran, An, Jiaxuan, Tang, Zhe, Sui, Guoqing, Wang, Makoto, Komiyama, Xingguo, Liang   +6 more
openaire   +2 more sources

Running Title: DNA replication and topology

, 2020
22 p.-5 fig.During replication, the topology of DNA changes continuously in response to well‐known activities of DNA helicases, polymerases, and topoisomerases.
Hernandez, Pablo, Schvartzman, Jorge Bernardo, Jorge B. Schvartzman, Pablo Hernández, Dora B. Krimer, Krimer, Dora B.   +5 more
core   +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

Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer

Molecular Oncology, EarlyView.
Tumors contain diverse cellular states whose behavior is shaped by context‐dependent gene coordination. By comparing gene–gene relationships across biological contexts, we identify adaptive transcriptional modules that reorganize into distinct vulnerability axes.
Brian Nelson, Lyanne Delgado‐Coka, Natalia Marchenko, Luisa F. Escobar‐Hoyos, Kenneth R. Shroyer, Alisa Yurovsky, Trey Ideker, Gábor Balázsi, Thomas MacCarthy, Scott Powers   +9 more
wiley   +1 more source