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Electric Transport and Coding Sequences of DNA Molecules

Explore the conductive properties of DNA, its potential as a molecular wire, and role in genetic coding sequences for molecular electronics. Experimental results and implications for DNA repair and nanotechnology. Assess diversified findings in DNA conductivity with a focus on sequence-dependent conductance.

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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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