Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies

Jae Young Lee, Yanggyun Kim, Do-Nyun Kim*

Nature Communications (2024), 15, 6446

[DOI]  [PDF]

DNA hydrogels with programmable condensation, expansion, and degradation for molecular carriers

Kyounghwa Jeon, Chanseok Lee, Jae Young Lee, Do-Nyun Kim*

ACS Applied Materials & Interfaces (2024), 16, 19, 24162–24171

[DOI]  [PDF]

Prediction of DNA origami shape using graph neural network

Chien Truong-Quoc†, Jae Young Lee†, Kyung Soo Kim, Do-Nyun Kim*

Nature Materials (2024), 23, 984–992

[DOI]  [PDF]

Controlling chiroptical responses via chemo-mechanical deformation of DNA origami structures

Taehwi Kim, Chanseok Lee, Jae Young Lee, Do-Nyun Kim*

ACS Nano (2024), 18, 4, 3414–3423

[DOI]  [PDF]

A computational model for structural dynamics and reconfiguration of DNA assemblies

Jae Young Lee, Heeyuen Koh, Do-Nyun Kim*

Nature Communications (2023), 14, 7079

[DOI]  [PDF]

Harnessing a paper-folding mechanism for reconfigurable DNA origami

Myoungseok Kim, Chanseok Lee, Kyounghwa Jeon, Jae Young Lee, Young-Joo Kim, Jae Gyung Lee, Hyunsu Kim, Maenghyo Cho, Do-Nyun Kim*

Nature (2023), 619, 78–86

[DOI]  [PDF]

Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy

Heng Ni†, Xiao Fan†, Feng Zhou, Galio Guo, Jae Young Lee, Nadrian C. Seeman, Do-Nyun Kim, Nan Yao*, Paul M. Chaikin*, Yimo Han*

iScience (2022), 25, 6, 104373

[DOI]  [PDF]

Formation of non-base-pairing DNA microgels using directed phase transition of amphiphilic monomers

Chanseok Lee†, Sungho Do†, Jae Young Lee, Minju Kim, Sang Moon Kim, Yongdae Shin*, Do-Nyun Kim*

Nucleic Acids Research (2022), 50, 7, 4187–4196

[DOI]  [PDF]

Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint

Jae Gyung Lee, Kyung Soo Kim, Jae Young Lee, Do-Nyun Kim*

ACS Nano (2022), 16, 3, 4289–4297

[DOI]  [PDF]

Characterizing and harnessing the mechanical properties of short single-stranded DNA in structured assemblies

Jae Young Lee†, Myoungseok Kim†, Chanseok Lee, Do-Nyun Kim*

ACS Nano (2021), 15, 12, 20430–20441

[DOI]  [PDF]

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Chanseok Lee†, Young-Joo Kim†, Kyung Soo Kim, Jae Young Lee, Do-Nyun Kim*

Nucleic Acids Research (2021), 49, 21, 12591–12599

[DOI]  [PDF]

Design approaches and computational tools for DNA nanostructures

Heeyuen Koh, Jae Gyung Lee, Jae Young Lee, Ryan Kim, Osamu Tabata, Jin-Woo Kim*, Do-Nyun Kim*

IEEE Open Journal of Nanotechnology (2021), 2, 86–100

[DOI]  [PDF]

Programming ultrasensitive threshold response through chemo-mechanical instability

Young-Joo Kim, Junho Park, Jae Young Lee, Do-Nyun Kim*

Nature Communications (2021), 12, 5177

[DOI]  [PDF]

Rapid computational analysis of structured DNA assemblies at near-atomic resolution

Jae Young Lee, Jae Gyung Lee, Giseok Yun, Chanseok Lee, Young-Joo Kim, Kyung Soo Kim, Tae Hwi Kim, Do-Nyun Kim*

ACS Nano (2021), 15, 1, 1002–1015

[DOI]  [PDF]

Tailoring the mechanical stiffness of DNA nanostructures using engineered defects

Chanseok Lee†, Kyung Soo Kim†, Young-Joo Kim, Jae Young Lee, Do-Nyun Kim*

ACS Nano (2019), 13, 7, 8329–8336

[DOI]  [PDF]

Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design

Jae Young Lee, Young-Joo Kim, Chanseok Lee, Jae Gyung Lee, Hiromasa Yagyu, Osamu Tabata, Do-Nyun Kim*

Nucleic Acids Research (2019), 47, 1, 93–102

[DOI]  [PDF]

A framework of finite element procedures for the analysis of proteins

Reza Sharifi Sedeh, Giseok Yun, Jae Young Lee, Klaus-Jürgen Bathe, Do-Nyun Kim*

Computers & Structures (2018), 196, 24–35

[DOI]  [PDF]

Polymorphic design of DNA origami structures through mechanical control of modular components

Chanseok Lee, Jae Young Lee, Do-Nyun Kim*

Nature Communications (2017), 8, 2067

[DOI]  [PDF]

Coarse-grained molecular dynamics model of double-stranded DNA for DNA nanostructure design

Hiromasa Yagyu*, Jae Young Lee, Do-Nyun Kim, Osamu Tabata

Journal of Physical Chemistry B (2017), 121, 19, 5033–5039

[DOI]  [PDF]

Ignition characteristics of laser-ablated aluminum at shock pressures up to 2 GPa

Kyung-Cheol Lee, Tsubasa Taira, Goon Mo Koo, Jae Young Lee, Jack J. Yoh*

Journal of Applied Physics (2014), 115, 013503

[DOI]  [PDF]

† Contributed equally,  * Corresponding author