Moon Jung (Luna) Kim

All Publications

• Protocol for covalent RNA labeling by RiboLight dyes for detection by in-gel fluorescence and fluorescence microscopy. STAR protocols Kim, M. J., Shin, J., Kool, E. T. 2026; 7 (2): 104579

  Abstract

  RNA abundance and localization provide key insights into cellular physiology and disease, making RNA a central target of basic and applied research. Here, we present a protocol for covalent labeling of RNA using RiboLight dyes for detection in gels and cells. We outline steps for cell culture, in vitro and cellular RNA labeling, sample purification, and visualization by in-gel fluorescence and fluorescence microscopy. This approach integrates readily into molecular and cellular biology workflows for RNA analysis. For complete details on the use and execution of this protocol, please refer to Shin et al.1.

  View details for DOI 10.1016/j.xpro.2026.104579

  View details for PubMedID 42133491

• Fluorogenic Covalent Probes for RNA. Journal of the American Chemical Society Shin, J., Kim, M. J., Kool, E. T. 2025

  Abstract

  Sequence-generalized fluorescent labels and stains for RNA can enable imaging, tracking, and analysis of the biopolymer. However, current noncovalent RNA dyes are poorly selective for RNA over DNA, interact weakly with their target, and can show limited utility in cellular RNA staining due to poor selectivity and high background signals. Here, we report a fluorogenic covalent labeling approach based on acylimidazole-mediated reaction of donor-acceptor fluorophores with 2'-hydroxyl (2'-OH) groups of RNA, providing a wavelength-tunable, sequence-independent strategy for selective labeling of the biopolymer. This reactive probe design enables labeling and imaging under mild aqueous conditions, providing up to 390-fold fluorescence enhancement and 970-fold selectivity for RNA over DNA, with four emission colors documented. The covalent fluorophore platform enables improved new tools for RNA-specific analysis and imaging in gels, in solution, and in living cells.

  View details for DOI 10.1021/jacs.5c14938

  View details for PubMedID 41267384

• Development of Highly Fluorogenic Styrene Probes for Visualizing RNA in Live Cells ACS CHEMICAL BIOLOGY Kim, M., Li, Y., Junge, J. A., Kim, N. K., Fraser, S. E., Zhang, C. 2023; 18 (7): 1523-1533

  Abstract

  Styrene dyes are useful imaging probes and fluorescent sensors due to their strong fluorogenic responses to environmental changes or binding macromolecules. Previously, indole-containing styrene dyes have been reported to selectively bind RNA in the nucleolus and cytoplasm. However, the application of these indole-based dyes in cell imaging is limited by their moderate fluorescence enhancement and quantum yields, as well as relatively high background associated with these green-emitting dyes. In this work, we have investigated the positional and electronic effects of the electron donor by generating regioisomeric and isosteric analogues of the indole ring. Select probes exhibited large Stokes shifts, enhanced molar extinction coefficients, and bathochromic shifts in their absorption and fluorescence wavelengths. In particular, the indolizine analogues displayed high membrane permeability, strong fluorogenic responses upon binding RNA, compatibility with fluorescence lifetime imaging microscopy (FLIM), low cytotoxicity, and excellent photostability. These indolizine dyes not only give rise to rapid, sensitive, and intense staining of nucleoli in live cells but can also resolve subnucleolar structures enabling highly detailed studies of nucleolar morphology. Furthermore, our dyes can partition into RNA coacervates and resolve the formation of multiphase complex coacervate droplets. These indolizine-containing styrene probes offer the highest fluorescence enhancement among the RNA-selective dyes reported in the literature; thus, these new dyes are excellent alternatives to the commercially available RNA dye, SYTO RNASelect, for visualizing RNA in live cells and in vitro.

  View details for DOI 10.1021/acschembio.3c00141

  View details for Web of Science ID 001012156500001

  View details for PubMedID 37200527

  View details for PubMedCentralID PMC10367048

• Optical Properties of New Donor-Acceptor Dyes for RNA Imaging: Insights from Ab Initio and Huckel's Model Calculations JOURNAL OF PHYSICAL CHEMISTRY B Giudetti, G., Li, Y., Kim, M., Zhang, C., Krylov, A. I. 2026

  Abstract

  Optical properties of 11 donor-acceptor dyes based on pyridinium-indole, pyridinium-indolizine, isoquinolinium-indole, and isoquinolinium-indolizine motifs developed for RNA imaging are investigated using high-level quantum chemistry methods and semiempirical Hückel's model. The goal of this study is 3-fold: (i) to develop and benchmark computational protocols that can be used for computational design and screening of novel dyes; (ii) to explain the trends in optical properties of the model dyes in terms of underlying charge distributions and connectivity; and (iii) to propose a strategy for tuning their optical properties by structural modifications. We also present the results for a new dye designed to have red-shifted absorption and emission.

  View details for DOI 10.1021/acs.jpcb.6c00667

  View details for Web of Science ID 001731658300001

  View details for PubMedID 41926647

• RNA 2'-OH modification with stable reagents enabled by nucleophilic catalysis. RSC advances Kool, E. T., Pratihar, S., Thacker, P. S., Banerjee, D., Kim, M. J., Shioi, R. 2025; 15 (43): 35749-35755

  Abstract

  RNA modification at 2'-OH has typically required highly reactive acylating species that exhibit short half-lives in water, challenging purification, and limiting shelf lives. Here, we investigate the use of more stable species as electrophilic reagents, employing nucleophilic catalysis to promote reactions. The results show that multiple previously unreported electrophiles can react in high stoichiometric yields with RNA under appropriate catalysis. Most notably, aryl esters can transfer acyl groups to RNA in one hour, but are stable for months even in pure water. The results expand the functional chemotypes of RNA-reactive species, and identify reagent classes with improved stability and selectivity.

  View details for DOI 10.1039/d5ra06314k

  View details for PubMedID 41018161

  View details for PubMedCentralID PMC12466920

• Nurturing the blossoming hydrogen economy using HBAT: modelling every link in the H₂ supply chain ENERGY & ENVIRONMENTAL SCIENCE Vargas, N., Kim, M., Vargas, C., Alfonso, D. F., Evans, J. T. 2024; 17 (3): 838-866

  View details for DOI 10.1039/d3ee02789a

  View details for Web of Science ID 001141028000001