Molecular Basis of Single-Walled Carbon Nanotube Recognition by Single-Stranded DNA," Daniel Roxbury, Jeetain Mittal, Anand Jagota(Nanoletters, 12  1464-1469 (2012))
Simulation of 3 strands of (TAT)4 on a (6,5) single-wall carbon nanotube.
(Moive by Daniel Roxbury & Jeetain Mittal )
Molecular simulation of beta-barrel DNA structures on SWNTs support the idea that such secondary structures are stabilized by their interaction with the nanotube core. (Journal of Physical Chemistry C, 2010, Roxbury et al.)
We have found recently that certain DNA sequences recognize specific carbon nanotubes. We have identified about 20 such special sequences. Using these, one can separate out each and every semiconducting CNT species from a mixture. The basis for recognition, we propose, is the formation of an ordered DNA structure stabilized by the CNT core. We have found that anti-parallel DNA strands can organize into ordered sheets similar to the beta-sheet structure of poly-peptides. Moreover, these can be rolled into barrels that resemble the protein beta-barrels. The experimental work on this project was conducted by X. Tu with M. Zheng; models were developed by S. Manohar with A. Jagota.
“DNA sequence motifs for structure-specific recognition and separation of carbon nanotubes”, Xiaomin Tu, Suresh Manohar, Anand Jagota, Ming Zheng, Nature v 460 250-253 (2009).
We have determined the charge density of dna-cnt hybrids by capillary electrophoresis measurements and have shown these are consistent with a dna beta-barrel model
“Measurement of Electrostatic Properties of DNA-Carbon Nanotube Hybrids by Capillary Electrophoresis,” C. Khripin, S. Manohar, M. Zheng, A. Jagota, Journal of Physical Chemistry C, DOI: 10.1021/jp903197d (2009)
DNA_CNT dynamics movie (also contains another unrelated experiment)
DNA-CNT Structure (S. Manohar & T. Tang)
The details of the structure of DNA-CNT hybrids determine how DNA helps to disperse and sort nanotubes. We have studied the structure using molecular dynamics (MD) simulations. Our results show that a significant fraction of bases come unstuck and that optimal helical wraps of DNA can be attained by a competition between electrostatic repulsion and base-CNT adhesion. The pictures below are from MD simulations and show some of these effects.
Many DNA bases unstuck from the CNT after equilibration in water.
Lateral motion of bases is relatively facile with a 2kT barrier between energy minima.
Suresh Manohar, Tian Tang, Anand Jagota, "Structure of Homopolymer DNA-CNT Hybrids, J. Phys. Chem. C, ASAP Article 10.1021/jp071316x S1932-7447(07)01316-7.