Carbon Nanotube and DNA/RNA Experiments and MD Simulation

DNA: Blueprint of Life DNA, gene, protein synthesis Replication, processing, transport, translation

Some Interesting Numbers DNA chains are incredibly long. A virus consists of about 200,000 nucleotides. A bacterium about 2 million. A human cell ~ BILLION (1,000,000,000)! If all DNA of one human cell were laid out straight, it would be about 1 yard long. If this DNA string is imagined as a flexible ladder, it would have about 6 billion steps. Human DNA is broken up into 46 chromosomes in each of our 6.3 trillion body cells.

Double Helix Structure of DNA Why the nitrogenous bases with organic rings are on the inside and sugar-phosphate chains are on the outside? Why a uniform diameter of the double helix excludes the like- with-like pairing of bases?

Abbreviations CNT: carbon nanotubes SWNT: single-walled nanotubes ssDNA: single-stranded DNA

Carbon Nanotube Very light and strong 10 times lighter but 250 times stronger than steel Thermal and chemical stability Highly conductive to heat and electricity 6 times more conductive than copper High mobility semiconductor More than 10,000 cm2/v.s Electric property extremely sensitive to environment a few molecules to single molecule level

CNT Application carbon nanotube properties Very light and strong 10 times lighter but 250 time stronger than steel Thermal and chemical stability Highly conductive to heat and Electricity 6 times more conductive than copper High mobility semiconductor More than 10,000 cm2/v.s Fast switch between on/off Electric property extreme sensitive to environment a few molecules to single molecule level Lighter and more conductive wire for electricity tranport

Types of SWCNT (n,m) Nanotube Naming Scheme Ch in an infinite graphene sheet describes how to "roll up" the graphene sheet. T is the tube axis. a1 and a2 are unit vectors of graphene in real space. A SWCNT is determined by a pair of indices (n,m): chiral vector C-C bond length 1.42 Å Ch = n a1 + m a2

Polarization Effect of the SWCNT Electrons of the SWCNT Dragged by a Passing Water Ion-SWCNT Terahertz Oscillator A potassium ion interacts with a 16Å carbon nanotube. The ion induces a strong dielectric response (polarizibility) in the nanotube wall. The motion of the ion naturally drags the electrons of the SWNT to oscillate at the same frequency. SWCNTs are highly polarizable due to their delocalized- electrons, which respond strongly to external fields.

I. ssDNA Wrapping Around SWCNT: Dispersion of CNT

Dispersion and Separation of CNT The CNT solubility is poor in both aqueous and non-aqueous solution. In practice SWNT are grown as mixtures of SWNT with different chiral vectors. For many applications, bundled CNT are required to disperse and separate.

ssDNA interacting with SWNT It was found that the ssDNA interacts strongly with SWNT to form a stable ssDNA-SWNT hybrid that effectively disperses SWNT in aqueous solution under sonication. M. Zheng, A. Jagota, E. D. Semke, et al, Nature Mater. 2, 338 (2003) N. Nakashima, S. Okuzono, H. Murakami, et al, Chem. Lett. 32, 456 (2003)

CNT: A Huge Conjugated System Benzene, C6H6: conjugated ring with 6 carbon atoms

DNA and RNA structure

Force Fields of CNT J. H. Walther, R. Jaffe, T. Halicioglu, and P. Koumoutsakos, J. Phys. Chem. B, 105, 9980 (2001) M. J. Bojan, and W. A. Steele, Langmuir, 3, 1123 (1987) the carbon-water potential

ssDNA and SWNT Left hand (6,4) SWNT with d=0.68 nm ssDNA: d(GT) 20

ssDNA-CNT with counter ion and a few layers of water molucules Case 1 The initial frame The final frame

Case 2 The initial frame The final frame

Case 3 The initial frame The final frame

ssDNA wrapping around SWNT AFM images of ssDNA-CNT hybrids M. Zheng, A. Jagota, E. D. Semke, et al, Nature Mater. 2, 338 (2003) M. Zheng, A. Jagota, M. S. Strano, et al, Science 302, 1545 (2003) AFM inages of CNT wrapped by d(GT) 30 showing regular helical pitch of ~18 nm.

II. DNA/RNA Transport Inside Individual SWCNT: High Throughput, Single- Molecule Probing Devices

Application of CNT as a TUBE MD simulation: Hummer, G. etc. Water conduction through the hydrophobic channel of a carbon nanotube. Nature 2001, 414, (6860), MD simulation: Kalra, A.etc. Osmotic water transport through carbon nanotube membranes. Proceedings of the National Academy of Sciences of the United States of America 2003, 100, (18),

Theoretical Prediction fluid transport through carbon nanotube How water transport inside carbon nanotube? Special H-bond, ice nanotube Nature 412, 802 (2001). How fast water and gas transport inside carbon nanotube? Water: ~1 meter/s Nature 414, 188 (2001) Nature 438, 44 (2005). Gas: orders of magnitude faster than diffusion in any known microporous adsorbent Physical Review Letters 89, /1 (2002). Nano Letters 6, (9), (2006). Ion transfer inside nanotube? Transfer rate is a function of external field. Journal of Chemical Physics 124, (20), / /8 (2006).

Translocation of DNA The electrophoretically- driven translocation of a 58- nucleotide DNA strand through the transmembrane pore of alpha-hemolysin, a self-assembling bacterial toxin. Aleksij Aksimentiev and Klaus Schulten, Biophysical Journal 88, (2005)

Theoretical Prediction Polynucleotide transport through SWCNT MD Simulation I.-C. Yeh, G. Hummer, Proceedings of the National Academy of Sciences of the United States of America 101, (2004).

Theoretical Prediction Polynucleotide transport through SWCNT MD Simulations shows that a DNA molecule could be spontaneously inserted into CNT in a water solute environment. Gao et al, Nanoletters, 3(4), (2003)

Experiment Single-stranded DNA and RNA molecules in solution can be driven through a nanoscopic pore by an applied electric field. As each molecule occupies the pore, a characteristic blockade of ionic current is produced. Deamer et al, Acc. Chem. Res., 35, (2003)

Acknowledgement Powerpoint slices from Yuhui Li and Jinyao Tang