Papers

Single-molecule imaging reveals the role of membrane-binding motif and C-terminal domain of RNase E in its localization and diffusion in Escherichia coli
Troyer L*, Wang Y-H*, Shobhna, Kim S, Woo J, Tajkhorshid E, and Kim S 2024.
[bioRxiv]

Re-defining how mRNA degradation is coordinated with transcription and translation in bacteria
Kim S, Wang Y-H, Hassan A, and Kim S 2024.
[bioRxiv]

DNA supercoiling drives a transition between collective modes of gene synthesis
Chatterjee P, Goldenfeld N, and Kim S Physical Review Letters, 2021.
[OpenAccess] [bioRxiv]

Probing mRNA kinetics in space and time in Escherichia coli using two-color single-molecule fluorescence in situ hybridization
Kim S and Vaidya K Journal of Visualized Experiments, 2020.
[OpenAccess] [github]

Better together: Cooperation and antagonism between RNA polymerases during transcription in vivo
Kim S Bioessays, 2020.
[PubMed] [OpenAccess]

Long-distance cooperative and antagonistic RNA polymerase dynamics via DNA supercoiling
Kim S, Beltran B, Irnov I, and Jacobs-Wagner C Cell, 2019.
[PubMed] [PDF] [github]

Nucleoid size scaling and intracellular organization of translation across bacteria
Gray WT, Govers SK, Xiang Y, Parry BR, Campos M, Kim S, and Jacobs-Wagner C Cell, 2019.
[PubMed] [PDF] [github]

Effects of mRNA degradation and site-specific transcriptional pausing on protein expression noise
Kim S and Jacobs-Wagner C Biophysical Journal, 2018.
[PubMed] [PDF] [Supp] [github]

Probing allostery through DNA
Kim S*, Broströmer E*, Xing D*, Jin J*, Chong S, Ge H, Wang S, Gu C, Yang L, Gao YQ, Su X-D, Sun Y, and Xie XS Science, 2013.
[PubMed] [PDF] [Supp]

Single-molecule study of DNA polymerization activity of HIV-1 reverse transcriptase on DNA template
Kim S, Schroeder CM, and Xie XS Journal of Molecular Biology, 2010.
[PubMed] [PDF] [Supp]

Hydrodynamic flow-stretching assay for single-molecule studies of nucleic acid–protein interactions
Schroeder CM, Blainey PC, Kim S, and Xie XS Single-Molecule Techniques: A Laboratory Manual, 2008.

Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA
Kim S, Blainey PC, Schroeder CM, and Xie XS Nature Methods, 2007.
[PubMed] [PDF] [Supp]

Direct observation of an intermediate state for a surface photochemical reaction initiated by hot electron transfer
Lee J, Ryu S, Chang J, Kim S, and Kim SK The Journal of Physical Chemistry B, 2005.
[PubMed]