a possible origin of semiconducting dna hiori kino(nims) masaru tateno(tit & aist) mauro...

A possible origin of semiconducting DNA

Hiori Kino(NIMS)

Masaru Tateno(TIT & AIST)

Mauro Boero(Univ. Tsukuba &AIST)

Jose Torres(Univ. Tsukuba)

Takahisa Ohno(NIMS)

Kiyoyuki Terakura(Univ. Hokkaido & AIST)

Hidetoshi Fukuyama(Univ. Tohoku)

•Introduction•DC conductivity measurements•Theoretical study so far•This work, theoretical study•Anderson localization

History

1. Radiation damageDNA is damaged by ultraviolet rays. “How does a hole or electron created by ultraviolet rays move in DNA?”→ electron transfer theory

2. Is DNA metallic or insulating?They measured DC conductivity.

Electron/hole hopping measurements in DNA

UV

If electrons/holes move rapidly, little radiation damage

DNA in a living body

HOMO(band)

LUMO(band)

UV light(trigger)

energy

Gap ~ 6-7eV

Motion of a existing hole/electron

DC transport measurement

I

dry DNA

V (trigger)

L

R

)()()( RFLF nnTdI (Landauer formula)

L

R

RLV

nF()

~Temperature

~T

If V is very small

Possibility of low energy excitation ~TWhere does a hole/electron come from?

Two kinds of exp.

HOMO(band)

LUMO(band)

UV light(trigger)

Chemicalpotential

energy

Gap ~ 6-7eV

~T

Electron transfer by UV light DC transport

Energy scale ~ 100eVEnergy scale < 102Kelvin

No density of states→No transportQ. Finite DOS at

Nano device?

•DNA : small crosssection (~2nm): self-assemble (utilizing complementary pairs of base molecules)

Figures, from C. Dekker, Phys. World. 14, 29 (2001).

•Low resistance useful nanowire

Seeman’s cubeHolliday junction

•Etching technology of ultra-fine structures will encounter the barrier in the near future

1.4kbase single-stranded DNA→octahedron

Another example

W.M. Shih, et al., Nature, 427, 618 (2004).

Diameter~14nm

Raw mages by cryo-electron microscopy

DNA gearJ. Am. Chem. Soc., 126 (37), 11410 -11411, 2004.“Molecular Gears: A Pair of DNA Circles Continuously Rolls against Each Other “Ye Tian and Chengde Mao*

DNA biped walking deviceNano Letters, 4 (7), 1203 -1207, 2004“A Precisely Controlled DNA Biped Walking Device “ (bike= 二本足歩行 )William B. Sherman and Nadrian C. Seeman*

DNA nano-machine

DC conductivity measurement

De Pablo et al. Phys. Rev. Lett. 85, 4992 (2000)

-DNA, scanning force microscopy~105cm (>70nm) (T=RT)

Bundle of DNA

Summary of Experiments

Fink et al., Nature 398, 407(1999)

Porath et al., Nature 403, 635(2000)

10-4cm(600nm-900nm),T=RT

10.4nm, T=100K-RT

-DNA

dG-dC

Cai, et al., APL 77 (2000) 3105

dG-dC

-DNA

Pablo et al. Phys. Rev. Lett. 85, 4992 (2000).

T=RT

T=RT

Yoo, et al. RPL 87 (2001) 198102

T=4.2K-RT

dG-dC

105cm (70nm)

1cm (50nm)

10-2cm (>20nm)

106cm (4m) -DNA

Zhang et al. Phys. Rev. Lett. 89, 198102-1 (2002).T=RT?

Metal,Insulator and doped semiconductor

Band gap~T*

~eV ~eV

E E E

E E

Impurity host

Thermally doped Intrinsically doped

metal insulator

schematically

semiconductor

Conductivity of semiconductor several order of magnitude depending on the density of impurities

Structure of DNA

PO4

base moleculesbackbone

• G:C, A:T= hydrogen bond

• PO4= -1 charged, DNA=negatively charged system at pH~7

• charge neutrality= cations (Na+, K+, Mg++,…)

Figures, from C. Dekker, Phys. World. 14, 29 (2001).

sugar

Theoretical Study

PW91/6-31G(d,p)

Electronic structure of base molecules

GpC: HOMO G LUMO C

ApT: HOMO A LUMO T

Blue=HOMO, Red=LUMOcompletely separated, G-C: hydrogen bonding

(acid) Poly(dG)-poly(dC) (PO4- is terminated by H+, the system is neutral)

Artacho et al. Mol. Phys. 101 (2003), 1587.DFT/GGA, SIESTA

→Insulating(gap~2eV), (LDA underestimates band gap.)

EF

CG

ij

jiij cctH e.g. HOMO band

Theoretical study (2)Electronic structure of DNA

G

C

Is semiconducting DNA possible?

~eV ~eV

E E

insulator semiconductor

There can be some methods to dope carriers into insulating DNA.

carriers!

E.g. P is added to dope carriers into insulating Si. ppm order of P is sufficient to make Si conducting.

Shift

Possible electronic structuresPoly(dG)-poly(dC)

HOMO(G)

LUMO(C)

(Without dopant)

DOS

(With dopant)

HOMO(G)

LUMO(C)

DOS(host)DOS(dopant)

hole

[(dG) 2

-X+?](X:impurity)

G

G

impurity

Intrinsic doping

Condition of DNA in experiments

GC

GC

DNA in solution

Dry DNA

Most cation metals are with solvation shells, some may be anhydrous

H2O

Possible loci of cations(study of effects of solvation shell of catons)

There are many possible loci of cations.There may be many possible loci of cations which dope carriers into DNA.

In this study, examine the electronic structure of one typical locus.

cation

DNA

Electronic structure of DNA hydrate v.s. anhydrous Mg

GC

[(dG)2Mg(H2O)n]+

PO4-1

Mg2+

Calc. UHF/6-31G(d)

(GGA/PBE gap~0.7eV)

(a)HOMO

LUMO

7.6 eV

Occupied stateB

(c)

G G(b)(a)

(c)

Unoccupied state

(b)Sz=0Mg2+

hydrated Mgcations

anhydrous Mgcation

LUMO

SOMO

(c’)

(b)

(a)(b)

(c’) Sz=1

(c’)

Mg+

LUMO@G

Schematic electronic structure of dry DNA

HOMO(G)

LUMO

DOS(host)DOS(dopant)

hole

[(dG) 2

-Mg2+]

G HOMO

impurity

poly(dG)-poly(dC)with anhydrous Mg

•Intrinsic doping = localized spin moment at Mg

# of injected holes into guanine HOMO band

# of anhydrous Mg=

A. degree of drying

Q. A possible origin of the diverse experimental results

Experimental suggestion of another method of doping I3

- , M. Taniguchi et al. Jpn. J. Apl. Phys. 42 (2003), L215

There will be a number of methods to dope carriers into insulating DNA chains.

c.f. P@Si, ppm order Very small # of injected holes can make DNA conducting

Maybe it is very hard to remove solvation shells.

Comment: doping a hole is different from moving of the hole easily

Other divalent cations Sz=0(para) Sz=0(AF) Sz=1(ferro) the most stable

A Mg -2604.691 -2604.700 -2604.725 ferroB Mg -2604.680 -2604.711 -2604.711 AF/ferro

A Zn -4182.521 -4182.581 -4182.555 AFB Zn -4182.482 -4182.546 -4182.536 AF

A Ca -3081.868 -3081.864 -3081.838 paraB Ca -3081.857 NG -3081.829 para

stru

ctur

eca

tion

GC

X PO4-

PO4-

X PO4-

X PO4-

PO4- X

PO4- Mg+

PO4- X

PO4- X

J

Intrinsic

Intrinsic

Thermal?

Doping mechanism

Band gap~T*EF

E E

Impurity Mother material

Unit: A.U., Gaussian 6-31G(d)/UHFabbreviation: A Mg = Mg@A-DNA

Anderson localization

•If DNA has doped one-dimensional band → Anderson localization •In one-dimension, no mobility edge → the wavefunction is always localized.•Long-ranged hopping mechanism → maybe variable range hopping (VRH)

E

(Assumption of VRH=doped band)

EF

band

Nonzero DOS at EF

Polaron and so on. may be necessary at higher temperatures. We do not deny their theories.At very low temperature, Anderson localization plays important roles.

I-V curve ---electronic contribution---

nTTA /100 )/(exp

n=dimension+1 Mott VRHn=2 Efros-Shklovskii(ES) VRH

Log

[ co

nduc

tivity

]

(103/T)1/2

Replot from Yoo, et al. RPL 87 (2001) 198102

n=2T0~90K (poly(dG)-poly(dC))

4.2K

Non-ohmic conductivity OK!

ndn

d

T

eE

T

TJ

R

T

ReE

TRJ

//1

0 cos2

1expcos~

/1~

2exp~

-1: localization length

Nonohmic threshold band gap

(V)

Stacked DNA into the gate

Exp. Yoo, et al. RPL 87 (2001) 198102.Theory. adopted the theory by H. Fukuyama and K. Yosida, J. Phys. Soc. Jpn. 46, 102 (1979).

Summary

•Intrinsic doping: Mg->ferro, Zn->antiferro•(Thermal doping: Ca ?)

Hydrated cation

Anhydrous cationHOMO

LUMO

SOMO

LUMO

An injected hole

J

00 SsJcctHij

jiij

# of doped holes= # of anhydrous Mg or Zn,

or thermally doped

(Longer chains must be calculated )

CommentsThe most stable structures of Mg@G2

Siesta (GGA+PCC): paramagnetic, HOMO=G, LUMO=MgGaussian98(HF): Ferromagnetic, SOMO=Mg, LUMO=GGuassian98(PW91PW91): Ferromagnetic, SOMO=Mg, LUMO=G

In STATE(ultrasoft PS, GGA) and CPMD(GGA), to achieve self-consistency is harder. Ferromagnetic solution seems to be the most stable.

Some LDA/GGA calculations of anhydrous Mg@DNA are unstable probably due to the self-interaction correction problem. Mg is spatially localized. Maybe it is connected with the result of siesta. Siesta uses localized PAOs which may raise the orbital energy of isolated Mg more than those of extended states of DNA base molecules. Careful consideration may be necessary to use PAOs in this case.

(G: guanosine)

Electronic structure of DNA (GGA/PBE)

GP

O-

O

G

Mg++

“Mg++”Paramag.(Sz=0)

G HOMO (ev)

EF

HOMO-1 HOMO LUMO

siesta

Doped semiconductors

1/T

Log[nc]

-1/2 Eg

-1/2(c-d)

(c-d)

Log

[ co

nduc

tivity

]

(103/T)1/2

Aschcroft and Mermin, Solid State Physics, page 580 on ‘Homogenious Semiconductors’

d

c

Eg

Replot from Yoo, et al. RPL 87 (2001) 198102

DOS

DNA exp.

textbook

a possible origin of semiconducting dna hiori kino(nims) masaru tateno(tit & aist) mauro...

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