Results 41 to 50 of about 22,006 (218)

Influence of supercoiling on the disruption of dsDNA

, 2004
We propose that supercoiling energizes double-stranded DNA (dsDNA) so as to facilitate thermal fluctuations to an unzipped state. We support this with a model of two elastic rods coupled via forces that represent base pair interactions.
Binney J. J., DiMarzio E. A., Paul M. Welch, Shirish M. Chitanvis, Sokolnikoff I. S., Wilsterman A. M.   +5 more
core   +1 more source

Nonlinear dynamic intertwining of rods with self-contact [PDF]

, 2007
Twisted marine cables on the sea floor can form highly contorted three-dimensional loops that resemble tangles. Such tangles or hockles are topologically equivalent to the plectomenes that form in supercoiled DNA molecules. The dynamic evolution of these
Goyal, Sachin, Lee, Christopher L., Perkins, N. C.   +2 more
core   +2 more sources

Amyloidogenic Peptide Fragments Designed From Bacterial Collagen‐like Proteins Form Hydrogel

Advanced Functional Materials, EarlyView.
This study identified amyloidogenic sequence motifs in bacterial collagen‐like proteins and exploited these to design peptides that self‐assemble into β‐sheet fibers and form hydrogels. One hydrogel supported healthy fibroblast growth, showing promise for biocompatible materials. Our work demonstrates that bacterial sequences can be harnessed to create
Vamika Sagar, Xuen J Ng, Lukas Lechel, Ashish Chand Rajwar, Hendrik Bargel, Abhishek A. Jalan   +5 more
wiley   +1 more source

Statistical Mechanics of Torque Induced Denaturation of DNA

, 1999
A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular structure. We show
A. Campa, C. Bouchiat, C. Cohen-Tannoudji, C. R. Calladine, D. Cule, E. W. Prohofsky, J. A. McCammon, J. F. Léger, J. F. Marko, J. F. Marko, M. Barbi, M. Peyrard, R. E. Depew, R. H. Austin, Rémi Monasson, Simona Cocco, T. Dauxois, T. R. Strick, T. R. Strick, T. R. Strick, W. Saenger, Y.-I. Zang   +21 more
core   +1 more source

Biological Consequences of Tightly Bent DNA: The Other Life of a Macromolecular Celebrity [PDF]

, 2006
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA persistence length ...
Garcia, Hernan G., Grayson, Paul, Han, Lin, Inamdar, Mandar, Kondev, Jane, Nelson, Philip C., Phillips, Rob, Widom, Jonathan, Wiggins, Paul A.   +8 more
core   +3 more sources

Dual‐Peptide Nanoplatform: Mesoporous Silica Nanoparticles Functionalized With a Cell‐Penetrating Peptide and Loaded With Rationally Designed Antimicrobial Peptides for Tuberculosis Therapy

Advanced Healthcare Materials, EarlyView.
Machine learning–guided engineering of a plectasin‐derived peptide yields DC05, a potent antimycobacterial candidate. Encapsulation into tuftsin‐functionalized mesoporous silica nanoparticles enhances intracellular delivery, stability, and activity against Mycobacterium tuberculosis while maintaining low cytotoxicity and minimal hemolysis. The combined
Christian S. Carnero Canales, Cesar Augusto Roque‐Borda, Ana Carolina Cerqueira Negri, Oswaldo Ramirez Delgado, Letícia Oliveira Catarin Nunes, Flávia Aparecida Resende, Hernane Barud, Norival Alves Santos‐Filho, Saulo Santesso Garrido, Karen Cristina Oliveira, Alexandra Ivo de Medeiros, Rafael Miguel Sábio, Fernando Rogério Pavan   +12 more
wiley   +1 more source

Profiling DNA supercoiling domains in vivo

Genomics Data, 2014
Transitions in DNA structure have the capacity to regulate genes, but have been poorly characterised in eukaryotes due to a lack of appropriate techniques.
Samuel Corless, Catherine Naughton, Nick Gilbert   +2 more
doaj   +1 more source

Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix

, 2017
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other
A Laio, A Rich, AV Vologodskii, AV Vologodskii, AV Vologodskii, C Matek, CJ Benham, FC Oberstrass, H Meng, J SantaLucia, JA Gebe, JF Marko, JF Marko, JW Alexander, K Klenin, K Klenin, M Manghi, M Newman, M Thanbichler, MC Lagomarsino, MY Sheinin, N Blot, N Metropolis, P Carrivain, PG Wu, R Vlijm, SM Mirkin, T Lepage, T Strick, TR Strick, VV Rybenkov, Z Bryant, Z Liu   +32 more
core   +1 more source

Assembling a True “Olympic Gel” From over 16 000 Combinatorial DNA Rings

Advanced Materials, EarlyView.
Olympic gels are an elusive class of soft matter, consisting of molecular networks held together purely by mechanically interlocked rings. Their topological structure promises unique properties and functions, but their synthesis has proven notoriously difficult.
Sarah K. Speed, Yu‐Hsuan Peng, Azra Atabay, Krishna Gupta, Toni Müller, Carolin Fischer, Ilka M. Hermes, Jens‐Uwe Sommer, Michael Lang, Elisha Krieg   +9 more
wiley   +1 more source

An improved method for large-scale preparation of negatively and positively supercoiled plasmid DNA

BioTechniques, 2009
A rigorous understanding of the biological function of superhelical tension in cellular DNA requires the development of new tools and model systems for study.
Marita C. Barth, Debra A. Dederich, Peter C. Dedon   +2 more
doaj   +1 more source