Honglue Shi

Dec 4, 2024 | nature.com | Yekaterina Shulgina |Marena Trinidad |Conner Langeberg |Hunter Nisonoff |Seyone Chithrananda |Petr Skopintsev | +7 more

AbstractStructured RNA lies at the heart of many central biological processes, from gene expression to catalysis. RNA structure prediction is not yet possible due to a lack of high-quality reference data associated with organismal phenotypes that could inform RNA function. We present GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB).

Oct 2, 2024 | biorxiv.org | Honglue Shi |KEVIN WASKO |Marena Trinidad |Noor Al-Sayyad

AbstractRNA-guided CRISPR-Cas enzymes initiate programmable genome editing by recognizing a 20-base-pair DNA sequence adjacent to a short protospacer-adjacent motif (PAM). To uncover the molecular determinants of high-efficiency editing, we conducted biochemical, biophysical and cell-based assays on S. pyogenes Cas9 (SpyCas9) variants with wide-ranging genome editing efficiencies that differ in PAM binding specificity.

Dec 19, 2023 | nature.com | Ainan Geng |Rohit Roy |Honglue Shi

AbstractSparse and short-lived excited RNA conformational states are essential players in cell physiology, disease, and therapeutic development, yet determining their 3D structures remains challenging. Combining mutagenesis, NMR spectroscopy, and computational modeling, we determined the 3D structural ensemble formed by a short-lived (lifetime ~2.1 ms) lowly-populated (~0.4%) conformational state in HIV-1 TAR RNA.

May 4, 2023 | dx.doi.org | Rohit Roy |Honglue Shi |Dawn K. Merriman |Ainan Geng

Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Am. Chem. Soc. 2023, XXXX, XXX Terms & Conditions Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses).

May 4, 2023 | pubs.acs.org | Rohit Roy |Ainan Geng |Honglue Shi |Dawn K. Merriman

Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Am. Chem. Soc. 2023, XXXX, XXX Terms & Conditions Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses).