Sequence-dependent DNA condensation as a driving force of DNA phase separation.

Kang H, Yoo J, Sohn BK, Lee SW, Lee HS, Ma W, Kee JM, Aksimentiev A, Kim H.

Nucleic Acids Res. 2018 Jul 19. doi: 10.1093/nar/gky639. [Epub ahead of print]


A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes.

Ohmann A, Li CY, Maffeo C, Al Nahas K, Baumann KN, Göpfrich K, Yoo J, Keyser UF, Aksimentiev A.

Nat Commun. 2018 Jun 21;9(1):2426. doi: 10.1038/s41467-018-04821-5.


A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems.

Yoo J, Li CY, Slone SM, Maffeo C, Aksimentiev A.

Methods Mol Biol. 2018;1811:209-229. doi: 10.1007/978-1-4939-8582-1_15.


New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.

Yoo J, Aksimentiev A.

Phys Chem Chem Phys. 2018 Mar 28;20(13):8432-8449. doi: 10.1039/C7CP08185E. Review.


Mono-allyloxylated Cucurbit[7]uril Acts as an Unconventional Amphiphile To Form Light-Responsive Vesicles.

Park KM, Baek K, Ko YH, Shrinidhi A, Murray J, Jang WH, Kim KH, Lee JS, Yoo J, Kim S, Kim K.

Angew Chem Int Ed Engl. 2018 Mar 12;57(12):3132-3136. doi: 10.1002/anie.201713059. Epub 2018 Feb 21.


Correction to Ion Channels Made from a Single Membrane-Spanning DNA Duplex.

Göpfrich K, Li CY, Mames I, Bhamidimarri SP, Ricci M, Yoo J, Mames A, Ohmann A, Winterhalter M, Stulz E, Aksimentiev A, Keyser UF.

Nano Lett. 2017 Jul 12;17(7):4548. doi: 10.1021/acs.nanolett.7b02430. Epub 2017 Jun 13. No abstract available.


Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations.

Yoo J, Aksimentiev A.

J Phys Chem Lett. 2016 Oct 6;7(19):3812-3818. Epub 2016 Sep 14.


Large-Conductance Transmembrane Porin Made from DNA Origami.

Göpfrich K, Li CY, Ricci M, Bhamidimarri SP, Yoo J, Gyenes B, Ohmann A, Winterhalter M, Aksimentiev A, Keyser UF.

ACS Nano. 2016 Sep 27;10(9):8207-14. doi: 10.1021/acsnano.6b03759. Epub 2016 Aug 23.


Ion Channels Made from a Single Membrane-Spanning DNA Duplex.

Göpfrich K, Li CY, Mames I, Bhamidimarri SP, Ricci M, Yoo J, Mames A, Ohmann A, Winterhalter M, Stulz E, Aksimentiev A, Keyser UF.

Nano Lett. 2016 Jul 13;16(7):4665-9. doi: 10.1021/acs.nanolett.6b02039. Epub 2016 Jun 29.


Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

Yoo J, Wilson J, Aksimentiev A.

Biopolymers. 2016 Oct;105(10):752-63. doi: 10.1002/bip.22868.


Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore.

Bhattacharya S, Yoo J, Aksimentiev A.

ACS Nano. 2016 Apr 26;10(4):4644-51. doi: 10.1021/acsnano.6b00940. Epub 2016 Apr 15.


Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation.

Yoo J, Kim H, Aksimentiev A, Ha T.

Nat Commun. 2016 Mar 22;7:11045. doi: 10.1038/ncomms11045.


De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation.

Maffeo C, Yoo J, Aksimentiev A.

Nucleic Acids Res. 2016 Apr 20;44(7):3013-9. doi: 10.1093/nar/gkw155. Epub 2016 Mar 14.


Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability.

Ngo TT, Yoo J, Dai Q, Zhang Q, He C, Aksimentiev A, Ha T.

Nat Commun. 2016 Feb 24;7:10813. doi: 10.1038/ncomms10813.


The structure and intermolecular forces of DNA condensates.

Yoo J, Aksimentiev A.

Nucleic Acids Res. 2016 Mar 18;44(5):2036-46. doi: 10.1093/nar/gkw081. Epub 2016 Feb 15.


Improved Parameterization of Amine-Carboxylate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields.

Yoo J, Aksimentiev A.

J Chem Theory Comput. 2016 Jan 12;12(1):430-43. doi: 10.1021/acs.jctc.5b00967. Epub 2015 Dec 16.


Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating.

Yoo J, Aksimentiev A.

J Phys Chem Lett. 2015 Dec 3;6(23):4680-7. doi: 10.1021/acs.jpclett.5b01964. Epub 2015 Nov 12.


Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field.

Li CY, Hemmig EA, Kong J, Yoo J, Hernández-Ainsa S, Keyser UF, Aksimentiev A.

ACS Nano. 2015 Feb 24;9(2):1420-33. doi: 10.1021/nn505825z. Epub 2015 Jan 30.


In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

Yoo J, Aksimentiev A.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20099-104. doi: 10.1073/pnas.1316521110. Epub 2013 Nov 25.


A comparison of coarse-grained and continuum models for membrane bending in lipid bilayer fusion pores.

Yoo J, Jackson MB, Cui Q.

Biophys J. 2013 Feb 19;104(4):841-52. doi: 10.1016/j.bpj.2012.12.043.

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