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J Phys Chem B 2021 Apr 5;125(14):3486-3493. Epub 2021 Apr 5.

Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.

Riboswitches are regulatory ribonucleic acid (RNA) elements that act as ligand-dependent conformational switches that recognize their cognate ligand via a binding pocket located in their aptamer domain. In the apo form, the aptamer domain is dynamic, requiring an ensemble representation of its structure. Here, as a proof-of-concept, we used solvent accessibility information to construct a pair of dynamical ensembles of the aptamer domain of the well-studied -adenosylmethionine (SAM) class-I riboswitch in the absence (-SAM) and presence (+SAM) of SAM. Read More

Open Life Sci 2020 24;15(1):848-859. Epub 2020 Nov 24.

Department of orthopedics, Shaoxing Shangyu People's Hospital, No. 517, Shimin Avenue, Baiguan Street, Shangyu District, Shaoxing, Zhejiang Province, 312300, China.

Circular RNA sterile alpha motif domain containing 4A (circSAMD4A) was found to be differentially expressed in osteosarcoma and contributed to the tumorigenesis of osteosarcoma. However, the role of circSAMD4A in doxorubicin (DXR) resistance of osteosarcoma is yet to be elucidated. Levels of circSAMD4A, microRNA (miR)-218-5p and Krüppel-like factor 8 (KLF8) were detected using quantitative reverse transcription-polymerase chain reaction. Read More

Nanomaterials (Basel) 2021 Mar 26;11(4). Epub 2021 Mar 26.

College of Physics and Electronics, Shandong Normal University, Jinan 250014, China.

We investigated the optical spin Hall effect (OSHE) of the light field from a closed elliptical metallic curvilinear nanoslit instead of the usual truncated curvilinear nanoslit. By making use of the characteristic bright spots in the light field formed by the noncircular symmetry of the elliptical slit and by introducing a method to separate the incident spin component (ISC) and converted spin component (CSC) of the output field, the OSHE manifested in the spot shifts in the CSC was more clearly observable and easily measurable. The slope of the elliptical slit, which was inverse along the principal axes, provided a geometric phase gradient to yield the opposite shifts of the characteristic spots in centrosymmetry, with a double shift achieved between the spots. Read More

Viruses 2021 Mar 2;13(3). Epub 2021 Mar 2.

Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany.

The SAM and HD domain-containing protein 1 (SAMHD1) is a dNTP triphosphohydrolase that plays a crucial role for a variety of different cellular functions. Besides balancing intracellular dNTP concentrations, facilitating DNA damage repair, and dampening excessive immune responses, SAMHD1 has been shown to act as a major restriction factor against various virus species. In addition to its well-described activity against retroviruses such as HIV-1, SAMHD1 has been identified to reduce the infectivity of different DNA viruses such as the herpesviruses CMV and EBV, the poxvirus VACV, or the hepadnavirus HBV. Read More

Mol Microbiol 2021 Apr 2. Epub 2021 Apr 2.

Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY, 10016, USA.

Although riboswitches have long been known to regulate translation initiation and transcription termination, a growing body of evidence indicates that they can also control bacterial RNA lifetimes by acting directly to hasten or impede RNA degradation. Ligand binding to the aptamer domain of a riboswitch can accelerate RNA decay by triggering a conformational change that exposes sites to endonucleolytic cleavage or by catalyzing the self-cleavage of a prefolded ribozyme. Alternatively, the conformational change induced by ligand binding can protect RNA from degradation by blocking access to an RNA terminus or internal region that would otherwise be susceptible to attack by an exonuclease or an endonuclease. Read More