Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.
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http://dx.doi.org/10.1088/0953-8984/27/35/354101 | DOI Listing |
FEBS J
January 2025
Department of Biological Sciences, Chungnam National University, Daejeon, Korea.
Previous studies have identified three families of knotted phytochrome photoreceptors in cyanobacteria. We describe a fourth type: 'hybrid' phytochromes with putative bilin-binding cysteine residues in both their N-terminal 'knot' extensions and cGMP-phosphodiesterase/adenylate cyclase/FhlA (GAF) domains, which we designate as dual-cysteine bacteriophytochromes (DCBs). Recombinant expression of DCBs in Escherichia coli yields photoactive phycocyanobilin (PCB) adducts with red/far-red photocycles similar to those of the GAF-Cys-containing cyanobacterial phytochromes (Cph1s).
View Article and Find Full Text PDFCrit Rev Biotechnol
January 2025
Centre of Excellence in Epigenetics, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, India.
G-quadruplex structures (GQSes) are the intricate molecular knots or marvels that play diverse roles in various cellular processes, such as replication, transcription, and translation, which regulate gene expression. Even though GQSes can be found throughout the genome, they are more prevalent in certain genomic regions like promoters and 5'-UTRs. This review discusses the functionality of GQSes across various regions of the genome and draws attention to the intriguing world of DNA and RNA GQSes.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand.
Meloidogyne enterolobii, a guava root-knot nematode, is a highly virulent pest in tropical and subtropical regions causing galls or knots in roots of diverse plant species posing a serious threat to agriculture. Managing this nematode is challenging due to limitations in conventional identification based on isolation and microscopic classification requiring expertise and time. A colorimetric and fluorescent LAMP assay using simplified extraction method targeting rDNA-ITS region was developed to detect M.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
December 2024
Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie St., 50-383, Wrocław, Poland.
J Chem Phys
December 2024
Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA.
Molecular dynamics calculations have been used to explore the influence of knots on the strength of a polymer strand. In particular, the mechanism of breaking 31, 41, 51, and 52 prime knots has been studied using two very different models to represent the polymer: (1) the generic coarse-grained (CG) bead model of polymer physics and (2) a state-of-the-art machine learned atomistic neural network (NN) potential for polyethylene derived from electronic structure calculations. While there is a broad overall agreement between the results on the influence of the pulling rate on chain rupture based on the CG and atomistic NN models, for the simple 31 and 41 knots, significant differences are found for the more complex 51 and 52 knots.
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