https://scholar.dgist.ac.kr/handle/20.500.11750/13652 2026-04-04T13:36:28Z 2026-04-04T13:36:28Z Kim, Seongmin Kim, Dahoon Kim, Yoori https://scholar.dgist.ac.kr/handle/20.500.11750/59937 2026-02-08T16:10:23Z 2025-08-31T15:00:00Z

Title: Metal-stabilized G-quadruplexes: biological insights and sensing applications Author(s): Kim, Seongmin; Kim, Dahoon; Kim, Yoori Abstract: Repeat sequences account for approximately 45% of the human genome, and can produce noncanonical DNA secondary structures that include G-quadruplexes (G4s). Among these, G4s are unique, in that their formation and stability are largely influenced by metal cations, such as Na+, K+, Ca2+, and Mg2+. These cations stabilize G4 structures, while also influencing their folding and biological activities. Interactions between G4s and metal ions affect key cellular processes that include transcription, replication, and genome stability. This review highlights the structural diversity and functional roles of G4s, and further explores how their ion-dependent properties have been harnessed for applications in biosensing and therapeutic development. Future research directions to advance G4-targeted technologies for both diagnostic and clinical use are also discussed.

2025-08-31T15:00:00Z Seo, Minseok Kim, Bokyung Shin, Hyogyung Kim, Jinwoo Lee, Jong-bong Ko, Young-ho Kim, Jin Hae Kim, Yoori https://scholar.dgist.ac.kr/handle/20.500.11750/59922 2026-02-08T16:10:22Z 2025-09-30T15:00:00Z

Title: Structural and dynamic basis of Ssp4-mediated DNA protection in foodborne bacterial spores Author(s): Seo, Minseok; Kim, Bokyung; Shin, Hyogyung; Kim, Jinwoo; Lee, Jong-bong; Ko, Young-ho; Kim, Jin Hae; Kim, Yoori Abstract: Clostridium perfringens forms metabolically dormant endospores that withstand extreme environmental conditions. Small acid-soluble proteins (SASPs) are ubiquitous DNA-binding proteins in endospores that promote resistance. While their protective role has been previously characterized, we aimed to provide further biophysical insight into the nature of these interactions, focusing on variant-specific structural dynamics through novel single-molecule and NMR approaches. Here, we characterize the DNA-binding properties and structural features of two Ssp4 variants using single-molecule fluorescence imaging and NMR spectroscopy along with electrophoretic mobility shift assays (EMSA). Both Ssp4 variants bind DNA cooperatively, but single-molecule analysis revealed preferential binding to GC-rich regions and significantly increased residence time in the presence of dipicolinic acid (DPA). NMR analysis reveals that an aspartic acid residue at position 36 (D36) stabilizes the Ssp4 structure, and its removal induces local structural perturbations without altering DNA affinity. Our findings provide molecular insights into how Ssp4 variants protect DNA in substantially dehydrated endospores and promote spore survival. © 2025 Elsevier B.V., All rights reserved.

2025-09-30T15:00:00Z Zhang, Hongshan Shi, Zhubing Banigan, Edward J. Kim, Yoori Yu, Hongtao Bai, Xiao-chen Finkelstein, Ilya J. https://scholar.dgist.ac.kr/handle/20.500.11750/46372 2025-07-25T03:25:15Z 2023-07-31T15:00:00Z

Title: CTCF and R-loops are boundaries of cohesin-mediated DNA looping Author(s): Zhang, Hongshan; Shi, Zhubing; Banigan, Edward J.; Kim, Yoori; Yu, Hongtao; Bai, Xiao-chen; Finkelstein, Ilya J. Abstract: Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, we present direct evidence that CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging, we demonstrate that a critical N-terminal motif of CTCF blocks cohesin translocation and DNA looping. The cryo-EM structure of the cohesin-CTCF complex reveals that this CTCF motif ahead of zinc fingers can only reach its binding site on the STAG1 cohesin subunit when the N terminus of CTCF faces cohesin. Remarkably, a C-terminally oriented CTCF accelerates DNA compaction by cohesin. DNA-bound Cas9 and Cas12a ribonucleoproteins are also polar cohesin barriers, indicating that stalling may be intrinsic to cohesin itself. Finally, we show that RNA-DNA hybrids (R-loops) block cohesin-mediated DNA compaction in vitro and are enriched with cohesin subunits in vivo, likely forming TAD boundaries. © 2023 Elsevier Inc.

2023-07-31T15:00:00Z Shin, Hyogyung Kim, Yoori https://scholar.dgist.ac.kr/handle/20.500.11750/45975 2025-07-25T04:07:25Z 2022-12-31T15:00:00Z

Title: Regulation of loop extrusion on the interphase genome Author(s): Shin, Hyogyung; Kim, Yoori Abstract: In the human cell nucleus, dynamically organized chromatin is the substrate for gene regulation, DNA replication, and repair. A central mechanism of DNA loop formation is an ATPase motor cohesin-mediated loop extrusion. The cohesin complexes load and unload onto the chromosome under the control of other regulators that physically interact and affect motor activity. Regulation of the dynamic loading cycle of cohesin influences not only the chromatin structure but also genome-associated human disorders and aging. This review focuses on the recently spotlighted genome organizing factors and the mechanism by which their dynamic interactions shape the genome architecture in interphase. © 2023 Informa UK Limited, trading as Taylor & Francis Group.

2022-12-31T15:00:00Z