Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography.

Lei Zhang,Dongsheng Lei,Jessica M Smith,Jiankang Liu,Zhuoyang Lu,Xing Zhang,Gang Ren,A Paul Alivisatos,Meng Zhang,Huimin Tong

doi:10.1038/ncomms11083

Abstract

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ∼2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.

Highlights

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties
We used cryo-electron microscopic (cryo-EM) and optimized NS (OpNS) methods to examine the same sample under -178 °C and room temperature, respectively, (Fig. 1)
We calculated its bending energy, which is only B10% of the above bending energy, and only B20% of the worm-like chain (WLC) prediction, suggesting that the smooth DNA is more stiff than the WLC prediction, and EM configurations. (iii) After submitting this smooth model for energy minimization using the nanoscale molecular dynamics version 2 (NAMD2) software package[30], we found that the bending energy was increased B4–5 times, nearly approaching the WLC

Summary

Introduction

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics. We use IPET, cryo-EM and our previously reported optimized NS (OpNS)[19,20] techniques to investigate the morphology and 3D structure of hybridized DNA-nanogold conjugates These conjugates were self-assembled from a mixture of two monoconjugates, each consisting of 84-bp single-stranded DNA and a 5-nm nanogold particle. By OpNS-ET imaging and IPET 3D reconstruction, we reconstruct a total of 14 density maps at a resolution of B2 nm from 14 individual doublestranded DNA (dsDNA)-nanogold conjugates Using these maps as constraints, we derive 14 conformations of dsDNA by projecting a standard flexible dsDNA model onto the observed maps using molecular dynamics (MD) simulations. The general features revealed by this experiment can be expected to occur in a broad range of DNA-assembled nanostructures and flexible proteins

Methods

Results

Conclusion