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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.

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Carbon nanotube and dna rna l.jpg

Carbon Nanotube and DNA/RNA

Experiments and MD Simulation


Dna blueprint of life l.jpg
DNA: Blueprint of Life

  • DNA, gene, protein synthesis

  • Replication, processing, transport, translation


Some interesting numbers l.jpg
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 l.jpg
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 l.jpg
Abbreviations

  • CNT: carbon nanotubes

  • SWNT: single-walled nanotubes

  • ssDNA: single-stranded DNA


Carbon nanotube l.jpg
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 l.jpg
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 l.jpg
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 determinedby a pair of indices (n,m): chiral vector

C-C bond length 1.42 ÅCh = n a1 + m a2

http://www.ks.uiuc.edu/Research/nanotube/


Polarization effect of the swcnt l.jpg
Polarization Effect of the SWCNT

SWCNTs are highly polarizable due to their delocalized-electrons, which respond strongly to external fields.

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.

Electrons of the SWCNT Dragged by a Passing Water

http://www.ks.uiuc.edu/Research/nanotube/



Dispersion and separation of cnt l.jpg
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 l.jpg
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 l.jpg
CNT: A Huge Conjugated System

Benzene, C6H6: conjugated ring with 6 carbon atoms

http://andromeda.rutgers.edu/~huskey/images/benzene_mo.jpg



Force fields of cnt l.jpg
Force Fields of CNT

the carbon-water potential

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)


Ssdna and swnt l.jpg
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 l.jpg
ssDNA-CNT with counter ion and a few layers of water molucules

Case 1

The initial frame

The final frame


Case 2 l.jpg
Case 2 molucules

The initial frame

The final frame


Case 3 l.jpg
Case 3 molucules

The initial frame

The final frame


Ssdna wrapping around swnt l.jpg
ssDNA wrapping around SWNT molucules

AFM inages of CNT wrapped by d(GT)30 showing regular helical pitch of ~18 nm.

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, Science302, 1545 (2003)


Ii dna rna transport inside individual swcnt high throughput single molecule probing devices l.jpg

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


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Application of CNT as a TUBE molucules

MD simulation:

Hummer, G. etc.

Water conduction through the hydrophobic channel of a carbon nanotube.

Nature 2001, 414, (6860), 188-90.

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), 10175-10180.


Theoretical prediction fluid transport through carbon nanotube l.jpg
Theoretical Prediction moluculesfluid 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/sNature 414, 188 (2001) Nature 438, 44 (2005).

Gas: orders of magnitude faster than diffusion in any known microporous adsorbentPhysical Review Letters 89, 185901/1 (2002). Nano Letters 6, (9), 2150-2153 (2006).

Ion transfer inside nanotube?

Transfer rate is a function of external field.Journal of Chemical Physics 124, (20), 204510/1-204510/8 (2006).


Slide24 l.jpg

Translocation of DNA molucules

The electrophoretically-driven translocation of a 58-nucleotide DNA strand through the transmembrane pore of alpha-hemolysin, a self-assembling bacterial toxin.

http://www.ks.uiuc.edu/Research/hemolysin/

Aleksij Aksimentiev and Klaus Schulten, Biophysical Journal88, 3745-3761 (2005)


Theoretical prediction polynucleotide transport through swcnt l.jpg

MD Simulation molucules

I.-C. Yeh, G. Hummer, Proceedings of the National Academy of Sciences of the United States of America101, 12177 (2004).

Theoretical PredictionPolynucleotide transport through SWCNT


Slide26 l.jpg

Theoretical Prediction moluculesPolynucleotide 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), 471-473 (2003)


Experiment l.jpg
Experiment molucules

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, 817-825 (2003)


Acknowledgement l.jpg
Acknowledgement molucules

  • Powerpoint slices from Yuhui Li and Jinyao Tang


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