title: Nanoscale Structure and Elasticity of Pillared DNA Nanotubes.
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 11 000 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.
authors.affiliation: Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bangalore 560012, India.
authors.forename: Himanshu
authors.initials: H
authors.lastname: Joshi
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Madras , Chennai 600 036, India.
authors.forename: Atul
authors.initials: A
authors.lastname: Kaushik
authors.affiliation: Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: Nadrian C
authors.initials: NC
authors.lastname: Seeman
authors.affiliation: Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bangalore 560012, India.
authors.forename: Prabal K
authors.initials: PK
authors.lastname: Maiti
mesh_terms: D004247:DNA; D004548:Elasticity; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D043942:Nanotubes; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA
keywords: DNA nanotubes; Holliday junctions; molecular dynamics; persistence length