### Abstract

We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we introduce a computational design to create an atomistic model of a 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically with two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation trajectories in the presence of explicit water and ions shows that these structures are stable and well behaved in all three geometries. Hydrogen bonding is well maintained for all variants of 6HB DNTs. From the equilibrium bending angle distribution, we calculate the persistence lengths of these tubes. The measured persistence lengths of these nanotubes are 10 μm, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. To have a quantitative understanding of the stretch modulus of these tubes, we carried out nonequilibrium steered molecular dynamics (SMD). The linear part of the force-extension plot gives a stretch modulus in the range 6500 pN for 6HB without pillars, which increases to 11000 pN for tubes with three pillars. The values of the stretch modulus calculated using contour length distribution obtained from equilibrium MD simulations are similar to those obtained from nonequilibrium SMD simulations. The addition of pillars makes these DNTs very rigid.

Original language | English (US) |
---|---|

Pages (from-to) | 7780-7791 |

Number of pages | 12 |

Journal | ACS Nano |

Volume | 10 |

Issue number | 8 |

DOIs | |

State | Published - Aug 23 2016 |

### Fingerprint

### Keywords

- DNA nanotubes
- Holliday junctions
- molecular dynamics
- persistence length

### ASJC Scopus subject areas

- Engineering(all)
- Materials Science(all)
- Physics and Astronomy(all)

### Cite this

*ACS Nano*,

*10*(8), 7780-7791. https://doi.org/10.1021/acsnano.6b03360

**Nanoscale Structure and Elasticity of Pillared DNA Nanotubes.** / Joshi, Himanshu; Kaushik, Atul; Seeman, Nadrian; Maiti, Prabal K.

Research output: Contribution to journal › Article

*ACS Nano*, vol. 10, no. 8, pp. 7780-7791. https://doi.org/10.1021/acsnano.6b03360

}

TY - JOUR

T1 - Nanoscale Structure and Elasticity of Pillared DNA Nanotubes

AU - Joshi, Himanshu

AU - Kaushik, Atul

AU - Seeman, Nadrian

AU - Maiti, Prabal K.

PY - 2016/8/23

Y1 - 2016/8/23

N2 - We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we introduce a computational design to create an atomistic model of a 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically with two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation trajectories in the presence of explicit water and ions shows that these structures are stable and well behaved in all three geometries. Hydrogen bonding is well maintained for all variants of 6HB DNTs. From the equilibrium bending angle distribution, we calculate the persistence lengths of these tubes. The measured persistence lengths of these nanotubes are 10 μm, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. To have a quantitative understanding of the stretch modulus of these tubes, we carried out nonequilibrium steered molecular dynamics (SMD). The linear part of the force-extension plot gives a stretch modulus in the range 6500 pN for 6HB without pillars, which increases to 11000 pN for tubes with three pillars. The values of the stretch modulus calculated using contour length distribution obtained from equilibrium MD simulations are similar to those obtained from nonequilibrium SMD simulations. The addition of pillars makes these DNTs very rigid.

AB - We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we introduce a computational design to create an atomistic model of a 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically with two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation trajectories in the presence of explicit water and ions shows that these structures are stable and well behaved in all three geometries. Hydrogen bonding is well maintained for all variants of 6HB DNTs. From the equilibrium bending angle distribution, we calculate the persistence lengths of these tubes. The measured persistence lengths of these nanotubes are 10 μm, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. To have a quantitative understanding of the stretch modulus of these tubes, we carried out nonequilibrium steered molecular dynamics (SMD). The linear part of the force-extension plot gives a stretch modulus in the range 6500 pN for 6HB without pillars, which increases to 11000 pN for tubes with three pillars. The values of the stretch modulus calculated using contour length distribution obtained from equilibrium MD simulations are similar to those obtained from nonequilibrium SMD simulations. The addition of pillars makes these DNTs very rigid.

KW - DNA nanotubes

KW - Holliday junctions

KW - molecular dynamics

KW - persistence length

UR - http://www.scopus.com/inward/record.url?scp=84983631036&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84983631036&partnerID=8YFLogxK

U2 - 10.1021/acsnano.6b03360

DO - 10.1021/acsnano.6b03360

M3 - Article

VL - 10

SP - 7780

EP - 7791

JO - ACS Nano

JF - ACS Nano

SN - 1936-0851

IS - 8

ER -