A system of so-called coloured symmetry transformations is introduced, in the basis of which all possible symmetry groups of a single strand DNA molecule taken as a genetic text are derived. A strict description of functionally important symmetrical sites, such as palindromes, complementary palindromes, direct repeats is given in terms of the group theory. Possible role of symmetrical fragments in genome is discussed.
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bioRxiv
September 2024
Department of Biochemistry and Molecular Biophysics, Washington University in Saint Louis School of Medicine, Saint Louis, MO 63110.
UvrD-family helicases are superfamily 1A motor proteins that function during DNA replication, recombination, repair, and transcription. UvrD family monomers translocate along single stranded (ss) DNA but need to be activated by dimerization to unwind DNA in the absence of force or accessory factors. However, prior structural studies have only revealed monomeric complexes.
View Article and Find Full Text PDFbioRxiv
June 2024
York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.
Single-stranded DNA bacteriophages of the family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut microbiome, where their diversity has been linked to various chronic health disorders. Despite the clear importance of microviruses, little is known about the molecular mechanism of host infection.
View Article and Find Full Text PDFHomologous recombination (HR) is a high-fidelity repair mechanism for double-strand breaks. Rad51 is the key enzyme that forms filaments on single-stranded DNA (ssDNA) to catalyze homology search and DNA strand exchange in recombinational DNA repair. In this study, we employed single-particle cryo-electron microscopy (cryo-EM) to ascertain the density map of the budding yeast Rad51-ssDNA filament bound to ADP-AlF , achieving a resolution of 2.
View Article and Find Full Text PDFNano Lett
May 2024
School of Physics and Wuhan National High Magnetic Field Center, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China.
The spin-orbit coupling (SOC), the dynamics of the nonequilibrium transport process, and the breaking of time-reversal and space-inversion symmetries have been regarded as key factors for the emergence of chirality-induced spin selectivity (CISS) and chirality-dependent spin currents in helix molecules. In this work, we demonstrated the generation of persistent CISS currents in various circular single-stranded DNAs and 3-helix proteins for the first time, regardless of whether an external magnetic flux is applied or not. This new CISS effect presents only in equilibrium transport processes, distinct from the traditional CISS observed in nonequilibrium transport processes and linear helix molecules; we term it as the PCISS effect.
View Article and Find Full Text PDFPLoS One
December 2023
Plant Virology Group, Latvian Biomedical Research and Study Centre, Riga, Latvia.
Ryegrass mottle virus (RGMoV; genus: Sobemovirus) is a single-stranded positive RNA virus with a 30 nm viral particle size. It exhibits T = 3 symmetry with 180 coat protein (CP) subunits forming a viral structure. The RGMoV genome comprises five open reading frames that encode P1, Px, a membrane-anchored 3C-like serine protease, a viral genome-linked protein, P16, an RNA-dependent RNA polymerase, and CP.
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