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Electric Transport and Coding Sequences of DNA Molecules
C. T. ShihDept. Phys., Tunghai University
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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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What is DNA? A Schematic View
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Coding/Noncoding region Not all DNA codes correspond to gene
s (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% co
des are junk and introns
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Motivation: Is DNA a good conductor?
Interbase hybridization of z orbitals → Conductor? (Eley and Spivey, Trans. Faraday Soc. 58, 411, 1962)
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Is DNA a molecular wire in biological system? Distance-independent charge transfer betw
een 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)
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Thymine Dimer
How proteins (involved in repairing DNA defects) sense these defects?
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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).
MutY MutY
MutY MutY
Healthy DNA
Broken DNA
electron
Courtesy: R. A. Römer, Univ. Warwick
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Is DNA a building block in molecular electronics?
Sequence dependent Self-assembly Can be build as nanowires with compl
ex geometries and topologies As template of nanoelectronic devices
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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.
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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, 2
002) Band-gap insulator (Porath et al., Nature 403, 635,
2000) Activated hopping conductor (Tran et al., PRL 85, 1
564, 2000) Induced superconductor (Kasumov et al., Science 2
91, 280, 2000)
Score Now – Superconductor: Conductor: Semiconductor: Insulator = 1:5:5:7
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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 electr
odes (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
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Higher T, larger gap
○: Sample #1 + : Sample #2 ● and △:
Sample #3, cooling and heating measurements
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Experiment 2: Superconductivity? Yu. Kasumov et al. Science 291, 280 (2000) Sample: -DNA (bacteria phage), length=16m Substrate: Mica Electrode: Rhenium/Carbon (Re/C) → SC with Tc~ 1K, normal R ~
100 Slit R ~ 1 G, with DNA R ~ several Ks
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Results: Measurement: 1 nA, 30 Hz Ohmic behavior over the tem
perature range Power-law fit for the R-T curv
e 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 f
or DNA1 and 2, negative for 3
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Endres et al., Rev. Mod. Phys. 76, 195, 2004
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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…)
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Effective Hamiltonian of the hole propagation
S. Roche, PRL 91, 108101 (2003) εn : hole energy for diff. base=8.24eV, 9.14eV, 8.87eV, a
nd 7.75eV for n=A,T,C,G, respectively
Zero temperature, t0=tm=1.eV, εm= εG
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Transmission Coefficient: Transfer Matrix Method
E: Energy of injected hole; T(E): Transmission coefficent
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Transmission Coefficient for Human Chromosome and Random Sequence
Main: Human Ch22 ChromosomeInset: Random Seq.
S. Roche et al., PRL 91, 228101 (2003)
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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+E to get T(E0,E0+E,W,i)
Moving the window along the sequences and calculate T(E0,E0+E,W,i) for all i
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Yeast 3
tDNA=1.0
tDNA=0.4
Randomized
Fitted by 0/w we Y3
R3
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Comparison between the Coding region and the Integrated Transmission
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t=1 eV
t=0.4 eV
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Overlap of T(W,i) and G(i) For particular W, both transmission a
nd 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 t
wo normalized vectors
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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:
N
i itNt
1
1
N
i itt1
2''
i
iGiWTW )("),(")(
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Yeast ChIII (310kbps), tDNA=1eV
(MAX,wG)=(0.1,240)
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tDNA=1eV
tDNA=0.8eV
tDNA=0.6eV
tDNA=0.4eV
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Yeast Ch VIII (526kbps)
(MAX,wG)=(0.08,200)
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(MAX,wG)=(-0.13,80)
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(MAX,wG)=(-0.08,50)
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Summary There are two parameters Max and wG which are characteris
tic 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?