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| http://dx.doi.org/10.4103/JCAS.JCAS_178_19 | DOI Listing |
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Unlabelled: Structural RNAs exhibit a vast array of recurrent short 3D elements involving non-Watson-Crick interactions that help arrange canonical double helices into tertiary structures. We present CaCoFold-R3D, a probabilistic grammar that predicts these RNA 3D motifs (also termed modules) jointly with RNA secondary structure over a sequence or alignment. CaCoFold-R3D uses evolutionary information present in an RNA alignment to reliably identify canonical helices (including pseudoknots) by covariation.
View Article and Find Full Text PDFUnlabelled: Cytoplasmic proteins must recruit to membranes to function in processes such as endocytosis and cell division. Many of these proteins recognize not only the chemical structure of the membrane lipids, but the curvature of the surface, binding more strongly to more highly curved surfaces, or 'curvature sensing'. Curvature sensing by amphipathic helices is known to vary with membrane bending rigidity, but changes to lipid composition can simultaneously alter membrane thickness, spontaneous curvature, and leaflet symmetry, thus far preventing a systematic characterization of lipid composition on such curvature sensing through either experiment or simulation.
View Article and Find Full Text PDFSpontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates.
Nat Commun
January 2025
Molecular and Cellular Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
Coronaviruses evade detection by the host immune system with the help of the endoribonuclease Nsp15, which regulates levels of viral double stranded RNA by cleaving 3' of uridine (U). While prior structural data shows that to cleave double stranded RNA, Nsp15's target U must be flipped out of the helix, it is not yet understood whether Nsp15 initiates flipping or captures spontaneously flipped bases. We address this gap by designing fluorinated double stranded RNA substrates that allow us to directly relate a U's sequence context to both its tendency to spontaneously flip and its susceptibility to cleavage by Nsp15.
View Article and Find Full Text PDFChiral Nanostructures from Artificial Helical Polymers: Recent Advances in Synthesis, Regulation, and Functions.
ACS Nano
January 2025
School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong 518172, P.R. China.
Helical structures such as right-handed double helix for DNA and left-handed α-helix for proteins in biological systems are inherently chiral. Importantly, chirality at the nanoscopic level plays a vital role in their macroscopic chiral functionalities. In order to mimic the structures and functions of natural chiral nanoarchitectures, a variety of chiral nanostructures obtained from artificial helical polymers are prepared, which can be directly observed by atomic force microscopy (AFM), scanning tunneling microscopy (STM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM).
View Article and Find Full Text PDFModulating Charge Transfer Kinetics along Poly Adenine: Chemical Modifications, Temperature, and Conformational Effects.
J Chem Theory Comput
January 2025
Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy.
The charge transfer (CT) reactions in nucleic acids are crucial for genome damage and repair and nanoelectronics using DNA as a molecular conductor. Previous experimental and theoretical works underlined the significance of nucleic acid structural dynamics on CT kinetics, requiring models that incorporate the dynamics of the nucleic acid, solvents, and counterions. Here, we investigated hole transfer kinetics in poly adenine single and double strands at various temperatures and the rate enhancement due to adenine-to-7-deazaadenine mutation by means of a QM/MM approach.
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