Electrons on the Double Helix:Electrons on the Double Helix: Charge Transport in DNA?Charge Transport in DNA?

A detour right off the start::

“This structure has novel features which are of considerable biological

interest”-Watson and Crick, Nature April

25, 1953.

Deoxyribonucleic Acid

•Structure proposed by Watson and Crick – 50 years ago•Double Helix-Ladder structure•Bicomplementary strands

DNA in our body

•Almost 2 meters per strand of DNA wound up at many different levels of structure in a single chromosome.

•Encodes the human genome

from Di Felice et al.

Unique H-bonding base-base coupling

•Guanine-Cytosine•Adenine-Thymine•Auto-recognition, self-assembly•Strong bonding between bases

Eley and Spivey (1962): noted that DNA shows resemblance to high mobility aromatic crystals TTF-TCNQ; suggested it as efficient structure for electron transfer.Charge TransferCharge transport (diffusion?)Electrical conductivity along stack?

DNA StructureDNA Structure

Why it could be important:- DNA damage repair- Bottom up electronics fabrication

The proposed conduction mechanism: charge transport across the bases

•Initial experiments (Barton group ‘93) showed possibility of long range charge transfer

•Fluorescent group quenched by electron acceptor 20-40 A away.•Transfer efficiency e-r with ~ 0.2A-1

•Counter to prevailing paradigm of transfer efficiency ~ 1.5 A-1 from Marcus theory.

•Perturbations to the base stack show that charge transfer is through base pairs•“Chemistry-at-a-distance” in other exp.•Long range mobile electrons makes possible interesting electronic effects on double helix. ‘-way’ – called ‘wire-like’

Charge Transfer along DNA stack?Charge Transfer along DNA stack?

“Ask not what physics can do for biology, ask what biology can do for physics” - Stan Ulam

Charge transfer at long distances is independent of the distance. Possibility of electrical conduction?

•Many attempts to measure DC transport across few DNA strands•Unlike charge transfer experiments, no consensus has emerged. •Extreme sensitivity to details

Fink and Schönenberger 1999 Metal 1MW/10mPorath et al. 1999 Semiconductor 1M/10mCai et al. 2000 Semiconductor >1010/100Kasomov et al. 2000 Metal/Super. 300k/1m Yoo et al. 2001 Semiconductor (polarons) De Pablo et al. 2000 Insulator >1012W/10mZhang et al. 2002 Insulator > 106(-cm)

•Contact Resistances?•Strong length effects?•Substrate interaction?•Large parameter space?•Residual salt •Weak links?•Damage from probe?

Physicists Get InvolvedPhysicists Get Involved

For randomly oriented DNA strands placed in a uniform electric field the loss W due to the motion of electric charges along the strands is, to a good approximation,given by

where V is the volume of the conducting medium (see below),E0 is the time averaged applied ac field at the position of the sample, the factor of 1/3 results from a geometricalaverage of random orientations of the DNA segments with respect to the direction of the applied uniform electric field, and s refers to the real part of the complex conductivity.

Ac ConductivityAny conducting wire acts like an antenna at ac

fields

P. Tran, B. Alavi and G.Gruner: Phys. Rev Lett (2000)

DNA vs linear chain organic conductors

(TMTSF)2PF6 dsDNA

ssDNA should behave differently

Optical conductivity of DNA and doped SiliconOptical conductivity of DNA and doped Silicon

0.1 1 10 100 1000

1E-3

0.01

0.1

1

10

100

1000

0.001 0.010 0.100 1.000

1 (

cm)

-1

Frequency (THz)

E. Helgren, Si:P, T=2Kn

D = 0.89x1018 cm-3

W. Dash et. al., Si, T=77KPhys. Rev., 99, 1151 (1955)

nD < 1015 cm-3

E. Helgren, Si:P, T=2Kn

D = 1.6x1018 cm-3

M. Rice et. al., Si:P, T=2KPRB, 23, 5472 (1981)

nD = 1.9x1018 cm-3

Photon Energy (eV)

0.01 0.1 1 10 100 10001E-3

0.01

0.1

1

10

100

10001E-4 1E-3 0.01 0.1 1

DNA UV data

DNA 5% R.H.

DNA 95% R.H.

Wittlin et. al.

1 (

cm)

-1

Frequency (THz)

Photon Energy (eV)

•Phenomenological similarity between doped semiconductor and DNA.

•High AC conductivity difficult to rationalize with low DC conductivityDipole Relaxation Losses in DNAM. Briman, N. P. Armitage,E. Helgren, and G. Gruner NANO LETTERS 2004Vol. 4, No. 4733-736

Phys Rev Lett Nov 2000

The model: fluctuating bases lead to time dependent transfer rate for electrons. This leads to a rate limiting factor for the charge diffusion.

Water per nucleotide can be correlated to humidity by Brauer-Emmett-Teller (1938) equation: “Adsorption of Gases in Multimolecular Layers”

Water molecules 2 (3) types

•1st layer characterized by binding energy 1

•2nd layer characterized by binding energy by L

•Also permanent 0th layer

The role of water

•Indistinguishability of dsDNA and ssDNA AC conductivity is evidence for no conduction between bases.

•Effects of hydration in dsDNA.Hydration itself; well described by BET equation.The conformational state of dsDNA also changes At high humidity some conduction might be due to an increase in base-base electron transfer.

•Evidence for water dipole absorption being a major contribution to the AC conductivity.

Briman, NPA, Helgren, Gruner (2004)NPA, Briman, Gruner (2004)

e-

Double strand DNA possibility for tunneling

between base pairs

single strand DNANo possibility for base-

base tunneling

e-

TeraHertz Absorption in DNATeraHertz Absorption in DNA

Single Molecule Rotation

Tetrahedral Cluster Rotation

Digression: Digression: Biexponential Debye Relaxation in HBiexponential Debye Relaxation in H22OO

•Electromagnetic absorption in water can be characterized by two separate dipole relaxation process.

•Single molecule rotation F=170 fs ~ 5 THz

•Collective motion of transient tetrahedrally coordinated water clusters D=8.5 ps ~ 0.15 THz

•ps timescales makes THz crucial

Dipole Relaxation Effects in DNADipole Relaxation Effects in DNA

•Conductivity normalized to the volume occupied by water is well-described biexponential Debye model.

•Low humidities is dominated by single molecule rotation.

•High humidities collective effects play a larger role.

•Consistent with low(no) base-base conduction

“Researchers from the University of California, Los Angeles, have hammered the final nail in the coffin.” -New Scientist, 2003