Article
Chemistry, Multidisciplinary
Chak Kui Wong, Chuyan Tang, John S. Schreck, Jonathan P. K. Doye
Summary: This study demonstrates the application of coarse-grained modeling combined with umbrella sampling to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. The approach is illustrated with examples of DNA nanotubes and DNA origami sheets. The ability to compute such landscapes is crucial for DNA mechanotechnology and understanding stress accumulation during the self-assembly process of origamis.
Article
Automation & Control Systems
Hongying Zhang
Summary: The article discusses the design of new biomedical robots based on the origami principle, highlighting two categories of origami patterns applicable to medical devices. However, due to the unevenness of the physical folding structure, analyzing mechanics becomes more complex.
IEEE-ASME TRANSACTIONS ON MECHATRONICS
(2022)
Article
Automation & Control Systems
Hongying Zhang
Summary: The origami principle can be applied to build compact actuators, deployable stents, and minimally invasive surgery devices. Traditional paper-based origami is converted to physical robots, which become complex and challenging to analyze, leading to the proposal of a computational model for analysis and simulation.
IEEE-ASME TRANSACTIONS ON MECHATRONICS
(2022)
Review
Oncology
Oleg Timofeev, Thorsten Stiewe
Summary: p53 is a DNA-binding protein that activates genes to suppress cancer cells, and its mutations, including cooperativity mutations, can lead to tumorigenesis. Understanding the structural basis of p53's DNA binding cooperativity is important for cancer therapy, as it plays a critical role in controlling cell fate decisions and tumor suppression. Research on p53 has provided insights into its function and potential personalized treatments for cancer patients with cooperativity mutations.
Article
Multidisciplinary Sciences
Brennan Ashwood, Michael S. Jones, Andrew L. Ferguson, Andrei Tokmakoff
Summary: DNA duplex stability is affected by cooperative interactions between adjacent nucleotides and is destabilized by abasic site, which splits the cooperativity in a short duplex into two segments and introduces additional barriers to hybridization. This study used temperature-jump infrared spectroscopy and molecular dynamics simulations to investigate the destabilization mechanism and hybridization dynamics caused by an abasic site in small DNA duplexes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Xiaolin Niu, Ruirui Sun, Zhifeng Chen, Yirong Yao, Xiaobing Zuo, Chunlai Chen, Xianyang Fang
Summary: The study reveals that the length of long-range pseudoknot in flaviviral xrRNA modulates the Mg2+-dependence and significantly impacts its folding, conformational dynamics, and Xrn1 resistance.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Weihua Mu, Jing Kong, Jianshu Cao
Summary: This study investigates the conformation-modulated kinetics of human glucokinase using a five-state kinetic model, revealing the non-Michealis-Menten correction term of activity and the violation of conformational detailed balance. Furthermore, the study reproduces and explains the resonance effect observed in human glucokinase, and shows quantitative agreement with experimental measurements. The analysis suggests the generality of kinetic cooperativity and resonance in a general chemical network beyond the five-state model.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Yongbing Zhao
Summary: TFSyntax is a database focusing on the arrangement of transcription factor binding sites, providing detailed TF binding maps and syntax information. It contains a large amount of data mapping transcription factor binding motifs, which is valuable for studying the mechanism of transcriptional regulation and the mechanism of regulatory DNA variants causing diseases.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Katerina Zakharova, Brian J. Caldwell, Shalya Ta, Carter T. Wheat, Charles E. Bell
Summary: Red beta is a protein from bacteriophage lambda that promotes repair of double-stranded DNA breaks through single-strand annealing. Lysine residues within the DNA binding domain were found to be critical for DNA binding and recombination in vitro and in vivo, while lysines within the C-terminal domain were mainly involved in recombination. Specific lysine residues, such as K61 and K148, played important roles in DNA annealing and oligomer formation, respectively.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Juan P. G. Villaluenga, Francisco Javier Cao-Garcia
Summary: Ligands can alter the properties of polymers, and our research focuses on developing an accurate kinetic model for the cooperative binding kinetics of large ligands. We found that cooperativity significantly affects the affinity of the ligands, and it can be achieved through increased binding affinity or decreased release affinity. Cooperativity is crucial for understanding and characterizing ligand binding processes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Mechanics
Larissa M. Fonseca, Marcelo A. Savi
Summary: This paper investigates the unit cell behavior and symmetries of the origami waterbomb pattern, establishing a reduced-order model based on an equivalent mechanism approach for kinematics analysis and using nonlinear finite element analysis for mechanical analysis. The results show that the rigid foldability hypothesis is crucial for the equivalence between the two descriptions.
Article
Mathematics
Ruben A. Hidalgo, Israel Morales
Summary: In this paper, we offer a concise argument to demonstrate that any countable group can be represented as the full group of automorphisms of a suitable compact origami by considering origamis on the Loch Ness monster.
ARCHIV DER MATHEMATIK
(2023)
Review
Biochemistry & Molecular Biology
Janusz Blasiak
Summary: DNA double-strand breaks (DSBs) are repaired by non-homologous end joining (NHEJ) and homologous recombination repair (HRR), with single-strand annealing (SSA) as another repair system that can lead to chromosomal translocations in cancer. Inhibition of RAD52, the master regulator of SSA, may be a potential strategy in cancer therapy. SSA may also modulate the efficacy of CRISPR genome editing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Matthew G. Reeves, Elodie Tailleur, Peter A. Wood, Mathieu Marchivie, Guillaume Chastanet, Philippe Guionneau, Simon Parsons
Summary: Crystal packing energy calculations are used to analyze a family of spin crossover complexes, revealing a linear relationship between transition abruptness and changes in intermolecular interaction energy in the crystal structures. Abrupt transitions are associated with significant stabilising and destabilising changes in intermolecular interaction energies. Different classes of SCO complexes exhibit varying trends in relation to transition abruptness.
Article
Biochemistry & Molecular Biology
Gat Krieger, Offir Lupo, Patricia Wittkopp, Naama Barkai
Summary: The study reveals that variations in noncoding regulatory sequences play a central role in transcription factor binding, especially when motif sequences are altered. Reciprocal gain and loss of binding sites can occur between related genes, with most interspecific differences remaining uncompensated.
Article
Chemistry, Multidisciplinary
Ismael Mullor Ruiz, Jean-Michel Arbona, Amitkumar Lad, Oscar Mendoza, Jean-Pierre Aime, Juan Elezgaray
Article
Biology
Jean-Michel Arbona, Arach Golder, Olivier Hyrien, Alain Arneodo, Benjamin Audit
Article
Chemistry, Multidisciplinary
Liliya A. Yatsunyk, Olivier Pietrement, Delphine Albrecht, Phong Lan Thao Tran, Daniel Renciuk, Hiroshi Sugiyama, Jean-Michel Arbona, Jean-Pierre Aime, Jean-Louis Mergny
Article
Chemistry, Physical
Jean Michel Arbona, Jean-Pierre Aime, Juan Elezgaray
JOURNAL OF CHEMICAL PHYSICS
(2012)
Article
Chemistry, Multidisciplinary
Jie Song, Jean-Michel Arbona, Zhao Zhang, Lei Liu, Erqing Xie, Juan Elezgaray, Jean-Pierre Aime, Kurt Vesterager Gothelf, Flemming Besenbacher, Mingdong Dong
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2012)
Article
Physics, Fluids & Plasmas
Jean Michel Arbona, Jean-Pierre Aime, Juan Elezgaray
Article
Cell Biology
Hua Wong, Jean-Michel Arbona, Christophe Zimmer
Article
Biotechnology & Applied Microbiology
Magali Hennion, Jean-Michel Arbona, Laurent Lacroix, Corinne Cruaud, Bertrand Theulot, Benoit Le Tallec, Florence Proux, Xia Wu, Elizaveta Novikova, Stefan Engelen, Arnaud Lemainque, Benjamin Audit, Olivier Hyrien
Article
Biochemistry & Molecular Biology
Sebastien Herbert, Alice Brion, Jean-Michel Arbona, Mickael Lelek, Adeline Veillet, Benoit Lelandais, Jyotsana Parmar, Fabiola Garcia Fernandez, Etienne Almayrac, Yasmine Khalil, Eleonore Birgy, Emmanuelle Fabre, Christophe Zimmer
Article
Biotechnology & Applied Microbiology
Jean-Michel Arbona, Sebastien Herbert, Emmanuelle Fabre, Christophe Zimmer