A detour right off the start:: Electrons on the Double Helix: Charge Transport in DNA?
Deoxyribonucleic Acid • Structure proposed by Watson and Crick – 50 years ago • Double Helix-Ladder structure • Bicomplementary strands “This structure has novel features which are of considerable biological interest” -Watson and Crick,NatureApril 25, 1953.
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
DNA Structure • Unique H-bonding base-base coupling • Guanine-Cytosine • Adenine-Thymine • Auto-recognition, self-assembly • Strong p-p 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 Transfer • Charge transport (diffusion?) • Electrical conductivity • along stack? from Di Felice et al.
Why it could be important: - DNA damage repair - Bottom up electronics fabrication
Charge Transfer along DNA stack? • 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-br with b ~ 0.2A-1 • Counter to prevailing paradigm of transfer efficiency b ~ 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. ‘p-way’ – called ‘wire-like’ “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?
Physicists Get Involved • 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/10m Porath et al. 1999 Semiconductor 1MW/10m Cai et al. 2000 Semiconductor >1010W/100 Kasomov et al. 2000 Metal/Super. 300kW/1m Yoo et al. 2001 Semiconductor (polarons) De Pablo et al. 2000 Insulator >1012W/10m Zhang et al. 2002 Insulator > 106(W-cm) • Contact Resistances? • Strong length effects? • Substrate interaction? • Large parameter space? • Residual salt • Weak links? • Damage from probe?
Ac Conductivity Any conducting wire acts like an antenna at ac fields 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 geometrical average 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. 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 Silicon • Phenomenological similarity between doped semiconductor and DNA. • High AC conductivity difficult to rationalize with low DC conductivity Dipole Relaxation Losses in DNA M. 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.
The role of water • 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 e1 • 2nd layer characterized by binding energy by eL • Also permanent 0th layer
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)
TeraHertz Absorption in DNA e- e- single strand DNA No possibility for base-base tunneling Double strand DNA possibility for tunneling between base pairs
Digression: Biexponential Debye Relaxation in H2O • Electromagnetic absorption in water can be characterized by two separate dipole relaxation process. • Single molecule rotation tF=170 fs ~ 5 THz • Collective motion of transient tetrahedrally coordinated water clusters tD=8.5 ps ~ 0.15 THz • ps timescales makes THz crucial Single Molecule Rotation Tetrahedral Cluster Rotation
Dipole 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