1 electric transport and coding sequences of dna molecules c. t. shih dept. phys., tunghai...
Post on 19-Dec-2015
219 views
TRANSCRIPT
![Page 1: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/1.jpg)
1
Electric Transport and Coding Sequences of DNA Molecules
C. T. ShihDept. Phys., Tunghai University
![Page 2: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/2.jpg)
計算科學專題 2
Outline
Introduction and Motivation Experimental Results The Coarse-Grained Tight-Binding
Model Sequence-Dependent Conductance
and the Gene-Coding Sequences Summary
![Page 3: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/3.jpg)
計算科學專題 3
What is DNA? A Schematic View
![Page 4: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/4.jpg)
計算科學專題 4
![Page 5: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/5.jpg)
計算科學專題 5
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
![Page 6: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/6.jpg)
計算科學專題 6
![Page 7: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/7.jpg)
計算科學專題 7
Motivation: Is DNA a good conductor?
Interbase hybridization of z orbitals → Conductor? (Eley and Spivey, Trans. Faraday Soc. 58, 411, 1962)
![Page 8: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/8.jpg)
計算科學專題 8
![Page 9: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/9.jpg)
計算科學專題 9
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)
![Page 10: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/10.jpg)
計算科學專題 10
Thymine Dimer
How proteins (involved in repairing DNA defects) sense these defects?
![Page 11: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/11.jpg)
計算科學專題 11
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
![Page 12: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/12.jpg)
計算科學專題 12
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
![Page 13: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/13.jpg)
計算科學專題 13
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.
![Page 14: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/14.jpg)
計算科學專題 14
![Page 15: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/15.jpg)
計算科學專題 15
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
![Page 16: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/16.jpg)
計算科學專題 16
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
![Page 17: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/17.jpg)
計算科學專題 17
Higher T, larger gap
○: Sample #1 + : Sample #2 ● and △:
Sample #3, cooling and heating measurements
![Page 18: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/18.jpg)
計算科學專題 18
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
![Page 19: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/19.jpg)
計算科學專題 19
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
![Page 20: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/20.jpg)
計算科學專題 20
Endres et al., Rev. Mod. Phys. 76, 195, 2004
![Page 21: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/21.jpg)
計算科學專題 21
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…)
![Page 22: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/22.jpg)
計算科學專題 22
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
![Page 23: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/23.jpg)
計算科學專題 23
Transmission Coefficient: Transfer Matrix Method
E: Energy of injected hole; T(E): Transmission coefficent
![Page 24: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/24.jpg)
計算科學專題 24GCGCGC…… (60bps)
![Page 25: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/25.jpg)
計算科學專題 25
Transmission Coefficient for Human Chromosome and Random Sequence
Main: Human Ch22 ChromosomeInset: Random Seq.
S. Roche et al., PRL 91, 228101 (2003)
![Page 26: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/26.jpg)
計算科學專題 26
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
![Page 27: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/27.jpg)
計算科學專題 27
![Page 28: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/28.jpg)
計算科學專題 28
Yeast 3
tDNA=1.0
tDNA=0.4
Randomized
Fitted by 0/w we Y3
R3
![Page 29: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/29.jpg)
計算科學專題 29
Comparison between the Coding region and the Integrated Transmission
![Page 30: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/30.jpg)
計算科學專題 30
t=1 eV
t=0.4 eV
![Page 31: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/31.jpg)
計算科學專題 31
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
![Page 32: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/32.jpg)
計算科學專題 32
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 )("),(")(
![Page 33: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/33.jpg)
計算科學專題 33
Yeast ChIII (310kbps), tDNA=1eV
(MAX,wG)=(0.1,240)
![Page 34: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/34.jpg)
計算科學專題 34
tDNA=1eV
tDNA=0.8eV
tDNA=0.6eV
tDNA=0.4eV
![Page 35: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/35.jpg)
計算科學專題 35
Yeast Ch VIII (526kbps)
(MAX,wG)=(0.08,200)
![Page 36: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/36.jpg)
計算科學專題 36
![Page 37: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/37.jpg)
計算科學專題 37
(MAX,wG)=(-0.13,80)
![Page 38: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/38.jpg)
計算科學專題 38
(MAX,wG)=(-0.08,50)
![Page 39: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/39.jpg)
計算科學專題 39
![Page 40: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/40.jpg)
計算科學專題 40
![Page 41: 1 Electric Transport and Coding Sequences of DNA Molecules C. T. Shih Dept. Phys., Tunghai University](https://reader033.vdocuments.site/reader033/viewer/2022052913/56649d385503460f94a12307/html5/thumbnails/41.jpg)
計算科學專題 47
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?