D.L. Cox, Department of Physics, UC Davis

Electronic Properties of biomolecules: Theoretical studies of

DNA in solution and biological

environments

Electronic Properties of biomolecules: Theoretical studies of

DNA in solution and biological

environments D.L. Cox, Department of

Physics, UC DavisCollaborations with : J.C. Lin Thirumalai group at U. Md.), R.R.P. Singh (UCD), R.G.

Endres (Imperial College), A. Huebsch, M.S. Swaroop and S.K. Pati (JNCASR

Bangalore)Support: NSF (Center for Theoretical Biological Physics and I2CAM), DOE

Computer Support: CTBP, JNCASR

D.L. Cox, Department of Physics, UC Davis

Collaborations with : J.C. Lin Thirumalai group at U. Md.), R.R.P. Singh (UCD), R.G.

Endres (Imperial College), A. Huebsch, M.S. Swaroop and S.K. Pati (JNCASR

Bangalore)Support: NSF (Center for Theoretical Biological Physics and I2CAM), DOE

Computer Support: CTBP, JNCASR

CTBP

Two short stories about electronic properties of DNA ``in solvation

environment’’

Two short stories about electronic properties of DNA ``in solvation

environment’’

[4Fe-4S]

MutY

DNA

Au

Au

DNA + water + counterions + Au: Metallization of G’s + band gap engineering

DNA + MutY repair protein:Damage sensing for repair?

Basic structure of biological (wet) B-DNA

Basic structure of biological (wet) B-DNA

Common themesCommon themes Need to rationalize diverse set of data! Complexity of DNA (need for stabilization by

water, counterions, plus fluctuations) not amenable to ab initio quantum MD (Carr-Parrinello)

Use a combination of classical MD + ab initio approximate (DFT) electronic structure to get at:

* conformation dependence of electronic structure/tunneling

* contribution of solvation energy to electron transfer energetics* range of conductance behaviors

Need to rationalize diverse set of data! Complexity of DNA (need for stabilization by

water, counterions, plus fluctuations) not amenable to ab initio quantum MD (Carr-Parrinello)

Use a combination of classical MD + ab initio approximate (DFT) electronic structure to get at:

* conformation dependence of electronic structure/tunneling

* contribution of solvation energy to electron transfer energetics* range of conductance behaviors

Is the field alive and kicking?Some ISI evidence…

Is the field alive and kicking?Some ISI evidence…

For the last one: good fit to exponential (R2 = 0.99) with doubling time of 2 years assuming kickoff at year 0 AB (after Barton)

For the last one: good fit to exponential (R2 = 0.99) with doubling time of 2 years assuming kickoff at year 0 AB (after Barton)

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.



Search on ``DNA andElectron/hole transfer’’

Search on ``DNA andElectronic structure’’



Search on ``DNA andConduct* … ‘’

BBAB BBAB BBAB

Why is it growing? Why is it growing?

Although DNA is unlikely to be used as a conductor itself (the mobility is low….), it remains a great tool for nanoscaffolding (Seeman, Mirkin, Kawai….) and when dressed up with other molecules or atoms it can be useful for optical and molecular electronic technologies (modified bases do increase mobility by 1-2 orders of mag-Kawai group)

DNA does have the chance to be electronically active in its own right, unlike proteins, and represents a ``hydrogen atom’’ for studying the role of emergent properties in conformational and atomic heterogeneity on conducting molecules in complex environments

Rationalizing the wealth of data from a variety of experiments is a great and interesting intellectual challenge!

Although DNA is unlikely to be used as a conductor itself (the mobility is low….), it remains a great tool for nanoscaffolding (Seeman, Mirkin, Kawai….) and when dressed up with other molecules or atoms it can be useful for optical and molecular electronic technologies (modified bases do increase mobility by 1-2 orders of mag-Kawai group)

DNA does have the chance to be electronically active in its own right, unlike proteins, and represents a ``hydrogen atom’’ for studying the role of emergent properties in conformational and atomic heterogeneity on conducting molecules in complex environments

Rationalizing the wealth of data from a variety of experiments is a great and interesting intellectual challenge!

Nanostructures from DNA—no controversy here! Use

hybridization as design control

Nanostructures from DNA—no controversy here! Use

hybridization as design control

Self Assembled Nanoparticle Networks(Mirkin group)

Programmed Self Assembled Cube Structure(N. Seeman lab)

3 and 4-way junctions (Niemeier lab)

So what kind of conductance can you get for DNA? Not terrific, but at best

close to Bechgaard salts (review: Endres, Cox, Singh, Rev. Mod. Phys.

76, 195 [2004])

So what kind of conductance can you get for DNA? Not terrific, but at best

close to Bechgaard salts (review: Endres, Cox, Singh, Rev. Mod. Phys.

76, 195 [2004])

Note: in these latter ``flatline’’ experiments, emerging consensus is that DNA partially unwinds and/or flattens, yielding Anderson localization.

``High conductance’’

``Semiconducting’’

``Flatliners’’

(biological)

K. Yoo

NO CONTACTS!similar results in free hanging bundles

So what is the best structure for conduction and how does it depend

upon water?

So what is the best structure for conduction and how does it depend

upon water?The

Winner!

What’s up? Competition between and bonding - near

cancellation in A-DNA

What’s up? Competition between and bonding - near

cancellation in A-DNA

Dependence upon twist and stretch

(see also recent work by Senthilkumar et al., JACS 2005)

Dependence upon twist and stretch

(see also recent work by Senthilkumar et al., JACS 2005)

Note: 0’s above measured to ambient twist separation of DNA

stack |

`Wetting’ your appetite: influence of water on

conductance

`Wetting’ your appetite: influence of water on

conductance

Expt: exponential increase of conductance with humidity (Kleine-Ostmann et al, App. Phys. Lett. [2006])

Theory: evidence from combined QM/MM of water assisted hole conduction from waters in minor grooves linking oxygens of bases (Tsukamoto et al., Chem. Phys. Lett. [2007])

Expt: exponential increase of conductance with humidity (Kleine-Ostmann et al, App. Phys. Lett. [2006])

Theory: evidence from combined QM/MM of water assisted hole conduction from waters in minor grooves linking oxygens of bases (Tsukamoto et al., Chem. Phys. Lett. [2007])

Short Story 1: ``Metallization of DNA’’ by Au electrodes and ``band gap engineering’’

Short Story 1: ``Metallization of DNA’’ by Au electrodes and ``band gap engineering’’

Interesting single molecule experiments II – Xu et al, Nano Lett 2004 – in water -- DNA = metal???

Interesting single molecule experiments II – Xu et al, Nano Lett 2004 – in water -- DNA = metal???

Study again with AMBER + SIESTA

(Mallajosyula et al., PRL 2008)

Study again with AMBER + SIESTA

(Mallajosyula et al., PRL 2008) Evolve DNA 10-mers with water and

counter ions via AMBER8 (18 Na+ and 3000 TiP3P waters)

Take average structure and prune waters and DNA to hexamers

Attach to model Au electrodes (each 48 atoms) with thiol linkers (on hollow site of Au[111])

Carry out SIESTA PBE GGA functional with double zeta polarized for Au, P, counterions, double zeta for DNA bases, single zeta for water

Evolve DNA 10-mers with water and counter ions via AMBER8 (18 Na+ and 3000 TiP3P waters)

Take average structure and prune waters and DNA to hexamers

Attach to model Au electrodes (each 48 atoms) with thiol linkers (on hollow site of Au[111])

Carry out SIESTA PBE GGA functional with double zeta polarized for Au, P, counterions, double zeta for DNA bases, single zeta for water

Result: DNA almost metallized by Au Result: DNA almost metallized by Au

With 0 = Au Fermi Energy

Gap = 0.0006 ev

Gap = 0.05 eV

Gap = 0.03 eV

Gap = 0.4 eV

Homos are extended For GCn case; AT

Intermediate breaks this

Simple picture - G is the most oxidizable base

(highest HOMO)

Simple picture - G is the most oxidizable base

(highest HOMO)

Further borne out by transmission and tunneling

estimate

Further borne out by transmission and tunneling

estimate• Surprise: higher transmission through GGATGG than GCGCGC• Depends upon detail of cross-strand hopping• Using superexchange theory gives reason- able estimate of decay and transmission co- efficients (decay rate ~ 0.54/angs. vs. expt. value of 0.42/angs.; TGGATGG ~ 1000 TGCATGC

TGCGCGC ~ 40 TGCATGC )

Role of waterRole of water

Stabilizes more highly conducting B-DNA structure

Screens DNA and reduces oxidation potentials allowing proximity of G-levels to Au Fermi energy

Stabilizes more highly conducting B-DNA structure

Screens DNA and reduces oxidation potentials allowing proximity of G-levels to Au Fermi energy

Short Story II: electrons in DNA damage sensing for repair? JC

Chin, DL Cox, RRP Singh Biophysical J, 2008

Short Story II: electrons in DNA damage sensing for repair? JC

Chin, DL Cox, RRP Singh Biophysical J, 2008

[4Fe-4S]

MutY

DNA

Relevance to biology? Relevance to biology?

Oxidative damage can lead to oxidized GG dimer. Damage site can be long distance from oxidation site (Barton et al; Giese et al), via direct electron transfer (tunneling) at distances < 20 angstroms, electron hopping past that.

Chemical attack can modify a G to an oxoG with extra O attached, which subsequently can mismatch with A on replication

Intervening damage disrupts DNA conductance/``damage/repair’’ at a distance Numerous experiments by Barton group have illustrated this basic principle

Oxidative damage can lead to oxidized GG dimer. Damage site can be long distance from oxidation site (Barton et al; Giese et al), via direct electron transfer (tunneling) at distances < 20 angstroms, electron hopping past that.

Chemical attack can modify a G to an oxoG with extra O attached, which subsequently can mismatch with A on replication

Intervening damage disrupts DNA conductance/``damage/repair’’ at a distance Numerous experiments by Barton group have illustrated this basic principle

G-G ``hot spot’’

On repair and damage proteinsOn repair and damage proteins

MutY: glycosylase found in bacteria (e. coli) with homologues in yeast, mammals. Locates and excises A’s which are mismatched to 8-oxyguanines (oxidatively damaged G’s)

Fe4S4 active cluster which is highly conserved-and remains intact-what is that for?

MutY: glycosylase found in bacteria (e. coli) with homologues in yeast, mammals. Locates and excises A’s which are mismatched to 8-oxyguanines (oxidatively damaged G’s)

Fe4S4 active cluster which is highly conserved-and remains intact-what is that for?

Structure of MutY monomer (Y. Guan et al, Nature Struc. Biol. 5, 1058 (1998))

BIG QUESTIONS:

How do proteins locate damage sites along DNA?

Is Diffusion enough (Berg-von Hippel)? Can there be remote sensing of damage by

use of electron transfer or migration disrupted by lesions?

BIG QUESTIONS:

How do proteins locate damage sites along DNA?

Is Diffusion enough (Berg-von Hippel)? Can there be remote sensing of damage by

use of electron transfer or migration disrupted by lesions?

Against other sensing models: Diffusion may be enough—there are lots of open questions (1d? Biased or nonbiased? 1d-3d combined? Time scales? Parallelization (lots of searchers)?

Electronic detection: (1) Protein-Protein redox couples , or (2) redox sensitive lesions.

Redox modulation of search: protein must slow in vicinity of binding site to facilitate recognition. Redox coupling could facilitate this.

Against other sensing models: Diffusion may be enough—there are lots of open questions (1d? Biased or nonbiased? 1d-3d combined? Time scales? Parallelization (lots of searchers)?

Electronic detection: (1) Protein-Protein redox couples , or (2) redox sensitive lesions.

Redox modulation of search: protein must slow in vicinity of binding site to facilitate recognition. Redox coupling could facilitate this.

Direct Evidence for electron assisted damage recognition? (E.M. Boon et al,

PNAS 100, 12543 (2003))

Direct Evidence for electron assisted damage recognition? (E.M. Boon et al,

PNAS 100, 12543 (2003))Scenario:

•Reduced MutY acts as `transmitter’ (e-

from Fe4S4

cluster), oxidized MutY as `receiver’.

•Once reduced, MutY detaches.

•Damage blocks e- transmission and MutY processes to damage site, recruits repair complex

•Experimental Evidence: current from MutY to end electrode, blocked by deliberate damage, altered by mutation at Fe-S site

•Theory: order of magnitude or more enhancement of search rate (K.E. Ericksen, arXiv.org:q-bio.BM/0311033, preprint, Nov. 2003)

Theory StrategyTheory Strategy For active regions of MutY (Fe-S cluster) and DNA (oxoG

+ surrounding bases) use SIESTA based quantum mechanics to compute energy changes

For passive regions, use AMBER MD to compute energy changes via free energy perturbation analysis (linear variable interpolating between MutY(2+)-OxoG(+) to MutY(3+)-OxoG(0)

Add these contributions to get free energies of rearrangement and free energy differences - schematically

MD,tot - MD,in + QM,in

For active regions of MutY (Fe-S cluster) and DNA (oxoG + surrounding bases) use SIESTA based quantum mechanics to compute energy changes

For passive regions, use AMBER MD to compute energy changes via free energy perturbation analysis (linear variable interpolating between MutY(2+)-OxoG(+) to MutY(3+)-OxoG(0)

Add these contributions to get free energies of rearrangement and free energy differences - schematically

MD,tot - MD,in + QM,in

A little math for the MD/QM

A little math for the MD/QM

Free energy perturbation: H() = (1-HMutY(++)-OxoG(+)+ HMutY(+++)-OxoG(0)

Free energy difference:

GMD = ∫dH(integral from 0 to 1)

Reorganization energy:

= (1/2){HH

Combination of energy differences G = GMD,tot - GMD,in + GQM,in

Free energy perturbation: H() = (1-HMutY(++)-OxoG(+)+ HMutY(+++)-OxoG(0)

Free energy difference:

GMD = ∫dH(integral from 0 to 1)

Reorganization energy:

= (1/2){HH

Combination of energy differences G = GMD,tot - GMD,in + GQM,in

Estimation of HDAEstimation of HDA

Use the pathways algorithm of Beratan and Onuchic implemented through the HARLEM program

HARLEM searches for optimal matrix element over all paths with the approximation

Use the pathways algorithm of Beratan and Onuchic implemented through the HARLEM program

HARLEM searches for optimal matrix element over all paths with the approximation

prefactor depending upon D-A bonds (energy units)

c = through covalent bond = 0.6

H = through H-bond = .36 e-1.7(R-2.8)

S = through solvent = 0.6 e-1.7(R-1.4)

R=bond separation in angstroms

Wild Type MutY-DNA Wild Type MutY-DNA Preference of electron transfer from MutY to

oxidized oxoG enhances binding of 3+ MutY in vicinity of oxoG

Most probable rate from MD + QM = 2.1 x 106 sec-1

Preference of electron transfer from MutY to oxidized oxoG enhances binding of 3+ MutY in vicinity of oxoG

Most probable rate from MD + QM = 2.1 x 106 sec-1

R149W mutation (kills MutY efficacy)

R149W mutation (kills MutY efficacy)

R is right on optimal electron transfer pathway-losing hydrogen bond to DNA hurts HAD

Estimate ketR149W/ket

WT = 1/8

R is right on optimal electron transfer pathway-losing hydrogen bond to DNA hurts HAD

Estimate ketR149W/ket

WT = 1/8


are needed to see this picture.QuickTime™ and a

TIFF (Uncompressed) decompressorare needed to see this picture.

L154F mutationL154F mutation

More subtle - extra F size expands MutY and increases DA distance

Factor of 2 decrease in optimal rates





L154F mutationL154F mutation







ConclusionConclusion

Preferential binding of MutY(3+) in vicinity

Of oxidized oxoguanine Enhanced Binding allows faster finding

of damage site.

Preferential binding of MutY(3+) in vicinity

Of oxidized oxoguanine Enhanced Binding allows faster finding

of damage site.

Summary: Summary: Au can `metallize’ G-rich n-mers explaining ohmic

behavior of GCGC.. DNA; AT insert induces tunneling Potential relevance of electron transfer in MutY

damage detection References: R.G. Endres, D.L. Cox, R.R.P. Singh, Rev. Mod. Phys. 76, 195

(2004)A. Huebsch, R.G. Endres, D.L. Cox, R.R.P. Singh, Phys. Rev.

Lett. 94, 178102 (2005)R.G. Endres, D.L. Cox, R.R.P. Singh, cond-mat/0201404SS Mallajosyula et al. PRL 101 176805 (2008)JC Lin, DL Cox, RRP Singh Biophys J. 95,3259 (2008)

Au can `metallize’ G-rich n-mers explaining ohmic

behavior of GCGC.. DNA; AT insert induces tunneling Potential relevance of electron transfer in MutY

damage detection References: R.G. Endres, D.L. Cox, R.R.P. Singh, Rev. Mod. Phys. 76, 195

(2004)A. Huebsch, R.G. Endres, D.L. Cox, R.R.P. Singh, Phys. Rev.

Lett. 94, 178102 (2005)R.G. Endres, D.L. Cox, R.R.P. Singh, cond-mat/0201404SS Mallajosyula et al. PRL 101 176805 (2008)JC Lin, DL Cox, RRP Singh Biophys J. 95,3259 (2008)

Documents

D.L. Cox, Department of Physics, UC Davis