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Electric Transport and Coding Sequences of DNA Molecules

Electric Transport and Coding Sequences of DNA Molecules. C. T. Shih Dept. Phys., Tunghai University. Outline. Introduction and Motivation Experimental Results The Coarse-Grained Tight-Binding Model Sequence-Dependent Conductance and the Gene-Coding Sequences Summary.

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Electric Transport and Coding Sequences of DNA Molecules

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  1. Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University

  2. Outline • Introduction and Motivation • Experimental Results • The Coarse-Grained Tight-Binding Model • Sequence-Dependent Conductance and the Gene-Coding Sequences • Summary

  3. What is DNA? A Schematic View

  4. Coding/Noncoding region • Not all DNA codes correspond to genes (proteins) • There are “junk” segments between genes • There are introns and exons in genes • Only exons related to genetic codes • In human genome, more than 98% codes are junk and introns

  5. Motivation: Is DNA a good conductor? • Interbase hybridization of pz orbitals → Conductor? (Eley and Spivey, Trans. Faraday Soc. 58, 411, 1962)

  6. Is DNA a molecular wire in biological system? • Distance-independent charge transfer between DNA-intercalated transition-metal complexes (Murphy et al., Science 262, 1025, 1993) • The conductance of DNA may related to the mechanism of healing of a thymine dimer defect (Hall et al., Nature 382, 731, 1996; Dandliker et al., Science 275, 1465, 1997)

  7. Thymine Dimer • How proteins (involved in repairing DNA defects) sense these defects?

  8. Do enzymes scan DNA using electric pulses? "DNA-mediated charge transport for DNA repair" E.M. Boon, A.L. Livingston, N.H. Chmiel, S.S. David, and J.K. Barton, Proc. Nat. Acad. Sci.100, 12543-12547 (2003). Healthy DNA electron MutY MutY Broken DNA MutY MutY Courtesy: R. A. Römer, Univ. Warwick

  9. Is DNA a building block in molecular electronics? • Sequence dependent • Self-assembly • Can be build as nanowires with complex geometries and topologies • As template of nanoelectronic devices

  10. Chen, J. and Seeman, N.C. (1991), Nature (London)350, 631-633. Zhang, Y. and Seeman, N.C. (1994), J. Am. Chem. Soc.116, 1661-1669.

  11. Experimental Results • The results are controversial – almost cover all possibilities (Endres et al., Rev. Mod. Phys. 76, 195, 2004) • Anderson insulator (Zhang et al., PRL 89, 198102, 2002) • Band-gap insulator (Porath et al., Nature 403, 635, 2000) • Activated hopping conductor (Tran et al., PRL 85, 1564, 2000) • Induced superconductor (Kasumov et al., Science 291, 280, 2000) Score Now – Superconductor: Conductor: Semiconductor: Insulator = 1:5:5:7

  12. Experiment 1: Semiconductor • D. Porath et al. Nature 403, 635 (2000) • I-V curves • Poly(G)-Poly(C) seq. (GC)15 • Length: 10.4 nm • Put the DNA between the electrodes (space = 8nm) by electrostatic trapping • Several check to confirm that “1” DNA molecule between the electrodes • Measurement under air, vacuum, and several temperature • Maximum current ~ 100 nA ~ 1012 electrons/sec Gap

  13. Higher T, larger gap • ○: Sample #1 • ＋: Sample #2 • ● and △: Sample #3, cooling and heating measurements

  14. Experiment 2: Superconductivity? • Yu. Kasumov et al. Science 291, 280 (2000) • Sample: l-DNA (bacteria phage), length=16mm • Substrate: Mica • Electrode: Rhenium/Carbon (Re/C) → SC with Tc~ 1K, normal R ~ 100 W • Slit R ~ 1 GW, with DNA R ~ several KWs

  15. Results: • Measurement: 1 nA, 30 Hz • Ohmic behavior over the temperature range • Power-law fit for the R-T curve for T>1K (Luttinger liquid behavior) • Exponent: -0.05, -0.03, -0.08 for DNA1, 2, and 3 respectively • At T~1K, R drops for DNA1, 2 • Critical field: ~ 1Tesla • Magnetoresistance: positive for DNA1 and 2, negative for 3

  16. Endres et al., Rev. Mod. Phys. 76, 195, 2004

  17. Reasons for Diversified Results • Contacts between electrode and DNA • Differences in the DNA molecules (length, sequence, number of chains…) • Effects of the environments (temperature, number of H2O, preparation and detection…)

  18. Effective Hamiltonian of the hole propagation • S. Roche, PRL 91, 108101 (2003) • εn : hole energy for diff. base=8.24eV, 9.14eV, 8.87eV, and 7.75eV for n=A,T,C,G, respectively • Zero temperature, t0=tm=1.eV, εm= εG

  19. Transmission Coefficient: Transfer Matrix Method E: Energy of injected hole; T(E): Transmission coefficent

  20. GCGCGC…… (60bps)

  21. Transmission Coefficient for Human Chromosome and Random Sequence Main: Human Ch22 Chromosome Inset: Random Seq. S. Roche et al., PRL 91, 228101 (2003)

  22. Transmission Analysis of Genomes • The lengths of complete genomic sequences are too long (in comparison with the electric propagation length) -> analyze subsequences instead • W: length (window size) of the subsequence which T(E) will be calculated • T(E,W,i): transmission coefficient of the subsequence from i-th to i+W-1-th base, with incident energy E • Integrate T(E,W,i) in the range E0→E0+DE to get T(E0,E0+DE,W,i) • Moving the window along the sequences and calculate T(E0,E0+DE,W,i) for all i

  23. Yeast 3 Fitted by Y3 tDNA=1.0 R3 tDNA=0.4 Randomized

  24. Comparison between the Coding region and the Integrated Transmission

  25. t=0.4 eV t=1 eV

  26. Overlap of T(W,i) and G(i) • For particular W, both transmission and coding (G(i)=1 if i is in the coding region, and =0 otherwise) are vectors in L-dimension (L: length of the seq.) • Normalize the two vectors • Calculating the scalar product of the two normalized vectors

  27. Overlap between T(W,i) and G(i) • T(W,i)=(t1, t2....ti,....tN) • The averaged transmission: • Let t’i=ti-<t>, and norm of t’: • t”i=t’i/|t’|, T”(W,i)=(t1”, t2”....ti”,.... t”N) • Similarly, normalize G(i) → G”(i) • Calc. the scalar product:

  28. Yeast ChIII (310kbps), tDNA=1eV (WMAX,wG)=(0.1,240) W

  29. tDNA=1eV tDNA=0.8eV tDNA=0.6eV tDNA=0.4eV

  30. Yeast Ch VIII (526kbps) (WMAX,wG)=(0.08,200)

  31. (WMAX,wG)=(-0.13,80)

  32. (WMAX,wG)=(-0.08,50)

  33. Summary • There are two parameters WMax and wG which are characteristic values for different species • The possible applications: • To locate the genes • To understand the relation between transport properties and coding • Relation to evolution and taxonomy • DNA defect and repair • Future Works: • Analysis for more genomes • Finite-temperature effects – flexibility of the DNA chain, interaction with phonons • Ionization potential for bases is sequence-dependent • More realistic (finer-grained) Hamiltonian • Interaction of carriers – Hubbard U?

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