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 Publications


     # Co-first author; *Corresponding author

A. Papers

51 .    J. B. Son#, S. Kim#, S. Yang#, Y. Ahn, N. K. Lee*, “Analysis of Fluorescent Proteins for Observing Single Gene Locus in a Live and Fixed Escherichia coli Cell”, J. Phys. Chem. B, in press (2024). Invited Article

50.     S.-Y. Son#, D.-W. Bae#, E. Kim#, B.-G. Jeong, M.-Y. Kim, S.-Y. Youn, S. Yi, G. Kim, J.-S. Hahn, N. K. Lee, Y. J. Yoon*, S.-S. Cha*, “Structural investigation of the docking domain assembly from trans-AT polyketide synthases”, Structure, in press (2024).

49.     T. Ha*, J. Fei, S. Schmid, N. K. Lee, R. L Gonzalez Jr, S. Paul, S. Yeou, “Fluorescence resonance energy transfer at the single-molecule level”, Nat. Rev. Methods Primers 4, 21 (2024).

48.     Y. Kim#, H. Kim#, J. B. Son#, M. Filatov, C. H. Choi, N. K. Lee*, D. Lee*, “Single-Benzene Dual-Emitters Harness Excited-State Antiaromaticity for White Light Generation and Fluorescence Imaging”Angew. Chem. Int. Ed., 62, e202302107 (2023).

47.     G. Yoo, Y.-K. Shin,* N. K. Lee*, “The role of α-synuclein in SNARE-mediated synaptic vesicle fusion”, J. Mol. Biol., 435, 16775 (2023).

46.     G. Yoo, H. J. An, S. Yeou, N. K. Lee*, α-Synuclein disrupts vesicle fusion by two mutant-specific mechanismsMol. Cells, 45, 806-819 (2022).

45.     J. Yi#, S. Yeou#, N. K. Lee*, "DNA bending force facilitates Z-DNA formation under physiological salt conditions", J. Am. Chem. Soc., 144, 29, 13137-13145 (2022).

44.     S. Yeou#, J. Hwang#, J. Yi, C. Kim, S.K. Kim, N. K. Lee*, "Cytosine methylation regulates DNA bendability depending on the curvature", Chem. Sci., 13, 7516-7525 (2022).

43.     S. Yeou, N. K. Lee*, "Single-molecule methods for investigating the double-stranded DNA bendability", Mol. Cells, 45, 33 (2022).

42.     Y. Cho#, H. J. An#, T. Kim, C. Lee*, N. K. Lee*, "Mechanism of Cyanine5 to Cyanine3 photoconversion and its application for high-density single-particle tracking in a living cell", J. Am. Chem. Soc., 143, 14125-14135 (2021).

* Selected for Spotlights on Recent JACS Publications: WATCHING CYANINE DYE IN LIVING CELLS.

41.      R. Khounlo, B. JD Hawk, T.-M. Khu, G. Yoo, N. K. Lee, J. Pierson, Y.-K. Shin, "Membrane binding of α-synuclein stimulates expansion of SNARE-dependent fusion pore", Front. Cell Dev. Biol. 9: 663431 (2021).

40.     S. Yeou*, N. K. Lee*, "Contribution of a DNA Nick to DNA Bendability Depending on the Bending Force", Bull. Kor. Chem. Soc. 42, 1151-1154 (2021). *invited contribution.

39.     G. Yoo, S. Yeou, J. B. Son, Y.-K. Shin, N. K. Lee*, “Cooperative inhibition of SNARE-mediated vesicle fusion by α-synuclein monomers and oligomers”, Sci. Rep. 11, 10955 (2021).

38.     E. Lerner et al.FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices”, eLife 10, e60416 (2021).

 

37.     D.‐K. Kim, Y. S. Kim, C. S. Kim, N. K. Lee*, “Method for the Rapid Screening of Drug Candidates Using Single‐Protein Tracking in a Living Cell”, Bull. Kor. Chem. Soc. 42, 393-397 (2021).

36. J. Hwang, J.-Y. Kim, C. Kim, S. Park, S. Joo, S. K. Kim*, N. K. Lee*, "Single-molecule observation of ATP-independent SSB displacement by RecO in Deinococcus radiodurans", eLife 9, e50945 (2020)

35. S. Yang#,  S. H. Kim#, D.-K. Kim, H. J. An, J. B. Son, A. H. Gynnå, N. K. Lee*, " Transcription and translation contribute to gene locus relocation to the nucleoid periphery in E.coli, Nat. Communications 10, 5131 (2019)

34. D.-H. Kim, S. Park, D.-K. Kim, M. G. Jeong, J. Noh, Y. Kwon, K. Zhou, N. K. Lee*, S. H. Ryu*, "Direct visualization of single-molecule membrane protein interactions in living cells", PLoS Biol. 16, 12 (2018)

33. B. Hellenkamp et al.Precision and accuracy of single-molecule FRET measurements-a worldwide benchmark study”, Nat. Methods 15, 669-676 (2018).

* Worldwide research for the accurate FRET based on our work published in Biophys. J (2005).

32. K. Sung, J. Park, Y. Kim, N. K. Lee, and S. K. Kim*, "Target specificity of Cas9 Nuclease via DNA Rearrangement Regulated by the REC2 Domain", J. Am. Chem. Soc. 140, 7778-7781 (2018).

31. M.-J. Kwak, D. Kim, H. Kim, C. Kim, J. W. Bowman, S. Kim, K. Joo, J. Lee, K. S. Jin, Y.-G. Kim, N. K. Lee, J. U. Jung, B.-H. Oh*, “Architecture of the type IV coupling protein complex of Legionella pneumophila”, Nat. Microbiol. 2, 17114 (2017).

30. D.-H. Kim#, D.-K. Kim#, K. Zhou#, S. Park, Y. Kwon, M. G. Jeong, N. K. Lee*, S. H. Ryu*, “Single particle tracking-based reaction progress kinetic analysis reveals a series of molecular mechanisms of cetuximab-induced EGFR processes in a single living cell”, Chem. Sci. 8, 4823 (2017).

29. S. Jung, J. Park, J. Bang, J.-Y. Kim, C. Kim, Y. Jeon, S. H. Lee, H. Jin, S. Choi, B. Kim, W. J. Lee, C.-G. Pack, J.-B. Lee, N. K. Lee, S. Kim*, “Light-Induced Fluorescence Modulation of Quantum Dot-Crystal Violet Conjugates: Stochastic Off–On–Off Cycles for Multicolor Patterning and Super-Resolution”, J. Am. Chem. Soc. 139, 7603 (2017).

28. O. Lee, C. Kim, J. Y. Kim, N. K. Lee*, W. Sung*, "Two conformational states in D-form DNAs: The effects of local denaturation", Sci.  Reports 6, 28239 (2016)

27. G. Shin#, D.-K. Kim#, J. Doh, D. Lee, N. K. Lee*, G. Y. Jung*, “High-Resolution Pluronic-filled Microchip CE-SSCP Analysis System via Channel Width Control”, Electrophoresis 37, 676-679 (2016).

 

26. H. S. Kim, H. N. Im, D. R. An, J. Y. Yoon, J. Y. Jang, S. Mobashery, D. Hesek, M. Lee, J. Yoo, M. Cui, S. Choi, C. Kim, N. K. Lee, S.-J. Kim, J. Y. Kim, G. Bang, B. W. Han, B. I. Lee, H. J. Yoon, S. W. Suh, “The cell-shape determining Csd6 protein from Helicobacter pylori constitutes a new family of L,Dcarboxypeptidase", J. Biol. Chem. 290, 25103-25117 (2015).

 

25. Y. R. Lim, J.-H. Kim, S. J. Park, G.-S. Yang, S. Song, S.-K. Chang, N. K. Lee, J. Sung, “Quantitative understanding of probabilistic behavior of living cells operated by vibrant reaction networks”,  Phys. Rev. X 5, 031014 (2015).​

24. C. Kim, O. Lee, J.-Y. Kim, W. Sung, N. K. Lee,* “Dynamic release of bending stress in short dsDNA by a kink and forks”, Angew. Chem. Int. Ed. 31, 8943-8947 (2015).

** VIP paper (top 5%)

 

 

 

23. J.-Y. Kim, C. Kim, N. K. Lee,* “Real-time submillisecond single-molecule FRET dynamics of freely diffusing molecules with liposome tethering”, Nat. Communications 6, 6992 (2015).  

* Highlighted in Nature Materials, "Single-molecule tracking Fretted diffusion" (Nature Materials 14, 556, 2015)

22. D.-H. Kim#, K. Zhou#, D.-K. Kim#, S. Park, J. Noh, Y. Kwon, D. Kim, N. W. Song, J.-B. Lee, P.-G. Suh, N. K. Lee*, S. H. Ryu,*  "Analysis of Interactions between the Epidermal Growth Factor Receptor and Soluble Ligands on the Basis of Single-Molecule Diffusivity in the Membrane of Living Cells", Angew. Chem. Int. Ed. 24, 7028-7032(2015).
 

21. Y-M Soh, F. Bürmann, H-C Shin, T. Oda, K. S. Jin, C. P. Toseland, C. Kim, H. Lee, S. J. Kim, M-S Kong, M-L Durand-Diebold, Y.-G.  Kim, H. M. Kim, N. K. Lee, M. Sato, B.-H. Oh, S. Gruber, “Molecular basis for SMC rod formation and its dissolution upon DNA binding”, Mol. Cell 57, 1-14 (2015).

20. S. Yang, S. H. Kim, Y. R. Lim, C. H. Kim, H. J. An, J-H Kim, J. Sung,* N. K Lee* “Contribution of RNA polymerase concentration variation to protein expression noise”, Nat. communications 5, 4761 (2014).

19. B. K Choi#, M. G. Choi#,  J.Y. Kim#,  Y. Yang, Y. Lai, D. H. Kweon, N. K. Lee,* Y. K. Shin* “Large α-Synuclein oligomers inhibit neuronal SNARE-mediated vesicle docking”, Proc. Natl. Acad. Sci. USA 110, 4087-4092 (2013).

BRIC 2013 학술 가치가 높은 연구 성과 Top 5 선정

18. J. Y. Kim#, B. K Choi,# M. G. Choi, S. A. Kim, Y. Lai, Y. K. Shin,* N. K Lee,*  “Solution single-vesicle assay reveals PIP2-mediated sequential actions of synaptotagmin-1 on SNAREs”, EMBO J. 31, 2144-2155  (2012).

BRIC 2012 학술 가치가 높은 연구 성과 Top 5 선정

 

17. C. H. Kim, J. Y. Kim, S. H. Kim, B. I. Lee, N. K. Lee,* “Direct characterization of protein oligomers and their quaternary structures by single-molecule FRET”, Chem. Comm. 48, 1138-1140 (2012).

16. N. K. Lee,* S. Park, M. H. Yoon, Z. H. Kim, S. K. Kim,* “Effect of ring torsion on intramolecular vibrational redistribution dynamics of 1,1’-binaphthyl and 2,2’-binaphthyl”, Phys. Chem. Chem. Phys. 14, 840-848 (2012).

15. N. K. Lee,# H. R. Koh,# K. Y. Han, J. Lee, S. K. Kim, “Single-molecule, real-time measurement of enzyme kinetics by alternating-laser excitation fluorescence resonance energy transfer”, Chem. Comm. 46, 4683 (2010). # equal contribution.

14. X. S. Xie, P. J. Choi, G-W Li, N. K. Lee, and G. Lia, “Single-Molecule Approach to Molecular Biology in Living Bacterial Cells”, Annu. Rev. Biophys. 37, 417 (2008).

13. N. K. Lee, H. R. Koh, K. Y. Han, and S. K. Kim, “Folding of 8-17 deoxyribozyme studied by three-color alternating-laser excitation of single-molecules”, J. Am. Chem. Soc. 129, 15526 (2007).

12. N. K. Lee, A. N. Kapanidis, H. R. Koh, Y. Korlann, S. O. Ho, N. Gassman, S. K. Kim, and S. Weiss, “Three-Color Alternating-Laser Excitation of Single Molecules: Monitoring Multiple Interactions and Distances”, Biophys. J. 92, 303 (2007).

* Highlighted in “Probes Light the Way for Advances in FRET”, Biophotonics, p30, February (2007).

11. J. H. Kim, N. K. Lee, S. H. Lee, S. Y. Han, and J. K. Song, “Ion core structures in anthracene anion tetramers”, Bull. Korean Chem. Soc. 27, 1453 (2006).

10. A. N. Kapanidis, T. A. Laurence, N. K. Lee, E. Margeat, X. Kong, and S. Weiss, “Alternating-Laser Excitation of Single Biomolecules”, Acc. Chem. Res. 38, 523 (2005).

9. N. K. Lee,# A. N. Kapanidis,# Y. Wang, X. Michalet, J. Mukhopadhyay, R. H. Ebright, and S. Weiss, “Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation” Biophys. J. 88, 2939 (2005).

8. N. K. Lee and S. K. Kim, “Ab initio-based Intermolecular Carbon-Carbon Pair Potentials for Polycyclic Aromatic Hydrocarbon Clusters", J. Chem. Phys. (Communication) 122, 031102 (2005).

7. A. N. Kapanidis,# N. K. Lee,# E. Margeat, T. Laurence, S. Doose, and S. Weiss, “Fluorescence-Aided Molecule Sorting: analysis of structure and interactions by alternating-laser excitation of single molecules”, Proc. Natl. Acad. Sci. USA 101, 8936 (2004).

* Highlighted in

(1) C&EN news, Science Concentrates, p30, June 7 (2004);

(2) “Alternating-laser excitation probes structures and interactions”, Biophotonics, p52, August (2004);

(3) “Single-molecule sorting”, Nat. Biotechnol. 22, 831 (2004).

6. J. K. Song, N. K. Lee, J. H. Kim, S. Y. Han, and S. K. Kim, "Anion Clusters of Anthracene, Ann- (n=1-16)”, J. Chem. Phys. 119, 3071(2003).

5. J. K. Song, N. K. Lee, and S. K. Kim, "Multiple Ion Cores in Anthracene Anion Clusters", Angew. Chem. Int. Ed. 42, 213 (2003).

4. J. K. Song, N. K. Lee, and S. K. Kim, "The Benzene-Naphthalene Anion: the Smallest Anion Complex of Aromatic Hydrocarbons", J. Chem. Phys. (Communication) 117, 9973 (2002). 

3. J. K. Song, N. K. Lee, and S. K. Kim, "Photoelectron Spectroscopy of Pyrazine Cluster Anions", J. Chem. Phys. 117, 1589 (2002).

2. N. K. Lee, S. Park, and S. K. Kim, “Ab Initio Studies on the van der Waals Complexes of Polycyclic Aromatic Hydrocarbons. II. Naphthalene Dimer and Naphthalene-Anthracene Complex", J. Chem. Phys. 116, 7910 (2002).

1. N. K. Lee, S. Park, and S. K. Kim, “Ab Initio Studies on the van der Waals Complexes of Polycyclic Aromatic Hydrocarbons. I. Benzene-Naphthalene Complex", J. Chem. Phys. 116, 7902 (2002).

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B. Book chapters

1. J. Y. Kim, B. K Choi, Y. K. Shin, N. K Lee,* “Solution single-vesicle assay by alternating-laser excitation”, Exocytosis Methods, Volume 83, pp 3-22 (2014)

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