Biology subjects

Park, S. h.

Publications and source records attributed to Park, S. h..

4 recordsLinked to original sources

bioRxiv2024

Geometry of Braided DNA Dictates Supercoiling Partition

DNA's helical structure requires the replisome to rotate relative to the parental DNA during replication, generating supercoiling that partitions ahead and behind the fork. The influence of DNA substrate geometry on supercoiling partitioning and torsional resistance remains unclear. Here, we have engineered DNA-braiding substrates with end separations found during replication, measured braiding torques using an angular optical trap, and interpreted the results using Monte Carlo simulations. A substrate with small separations readily initiates braiding, suggesting that the fork would rotate during replication, partitioning supercoiling behind the replisome and reducing torsional resistance. In contrast, a substrate with a substantial separation at one end imposes a pronounced "torsional barrier" that hinders braiding initiation, suggesting a lack of fork rotation during replication, so supercoiling would partition ahead of the replisome. Our findings reveal a physical mechanism in which DNA fork geometry could modulate replisome dynamics, manage topological stress, and regulate replication progression in vivo.

biophysics↗

bioRxiv2024

An Effective Surface Passivation Assay for Single-Molecule Studies of Chromatin and Topoisomerase II

For single-molecule studies requiring surface anchoring of biomolecules, a poorly passivated surface can result in alterations of biomolecule structure and function that can result in artifacts. This protocol describes surface passivation and sample chamber preparation for mechanical manipulation of chromatin fibers and characterization of topoisomerase II activity in physiological buffer conditions. The method employs enhanced surface hydrophobicity and purified blocking proteins to reduce non-specific surface adsorption. This method is accessible, cost-effective, and potentially widely applicable to other biomolecules. For a complete list of publications that employ this protocol, see the paper references. B. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/614989v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@d52b73org.highwire.dtl.DTLVardef@117bfc3org.highwire.dtl.DTLVardef@2eb670org.highwire.dtl.DTLVardef@cb88b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Chromatinization Modulates Topoisomerase II Processivity

Type IIA topoisomerases are essential DNA processing enzymes that must robustly and reliably relax DNA torsional stress in vivo. While cellular processes constantly create different degrees of torsional stress, how this stress feeds back to control type IIA topoisomerase function remains obscure. Using a suite of single-molecule approaches, we examined the torsional impact on supercoiling relaxation of both naked DNA and chromatin by eukaryotic topoisomerase II (topo II). We observed that topo II was at least [~] 50-fold more processive on plectonemic DNA than previously estimated, capable of relaxing > 6000 turns. We further discovered that topo II could relax supercoiled DNA prior to plectoneme formation, but with a [~]100-fold reduction in processivity; strikingly, the relaxation rate in this regime decreased with diminishing torsion in a manner consistent with the capture of transient DNA loops by topo II. Chromatinization preserved the high processivity of the enzyme under high torsional stress. Interestingly, topo II was still highly processive ([~] 1000 turns) even under low torsional stress, consistent with the predisposition of chromatin to readily form DNA crossings. This work establishes that chromatin is a major stimulant of topo II function, capable of enhancing function even under low torsional stress.

biophysics↗

bioRxiv2019

Cryo-EM structure of the human Mixed Lineage Leukemia-1 complex bound to the nucleosome

Mixed Lineage Leukemia (MLL) family histone methyltransferases are the key enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive structural and biochemical studies, the molecular mechanism by which the MLL complexes recognize histone H3K4 within the nucleosome core particle (NCP) remains unclear. Here, we report the single-particle cryo-electron microscopy (cryo-EM) structure of the human MLL1 core complex bound to the NCP. The MLL1 core complex anchors on the NCP through RbBP5 and ASH2L, which interacts extensively with nucleosomal DNA as well as the surface close to histone H4 N-terminal tail. Concurrent interactions of RbBP5 and ASH2L with the NCP uniquely align the catalytic MLL1SET domain at the nucleosome dyad, allowing symmetrical access to both H3K4 substrates within the NCP. Our study sheds light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity.

biochemistry↗