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

1. CTBP Electronic Properties of biomolecules: Theoretical studies of DNA in solution and biological environments 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

2. MutY DNA [4Fe-4S] Two short stories about electronic properties of DNA ``in solvation environment’’ Au Au DNA + water + counterions + Au: Metallization of G’s + band gap engineering DNA + MutY repair protein: Damage sensing for repair?

3. Basic structure of biological (wet) B-DNA

4. Common 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

5. Is the field alive and kicking?Some ISI evidence… BBAB BBAB BBAB Search on ``DNA and Electron/hole transfer’’ Search on ``DNA and Electronic structure’’ Search on ``DNA and Conduct* … ‘’ • 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)

6. 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!

7. Nanostructures from DNA—no controversy here! Use hybridization as design control 3 and 4-way junctions (Niemeier lab) Self Assembled Nanoparticle Networks (Mirkin group) Programmed Self Assembled Cube Structure (N. Seeman lab)

8. 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]) ``High conductance’’ ``Semiconducting’’  ``Flatliners’’ Note: in these latter ``flatline’’ experiments, emerging consensus is that DNA partially unwinds and/or flattens, yielding Anderson localization.

9. K. Yoo (biological) NO CONTACTS! similar results in free hanging bundles

10. So what is the best structure for conduction and how does it depend upon water? The Winner!

11. What’s up? Competition between p and s bonding - near cancellation in A-DNA

12. Dependence upon twist and stretch(see also recent work by Senthilkumar et al., JACS 2005) stack | Note: 0’s above measured to ambient twist separation of DNA

13. `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])

14. 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???

15. 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

16. 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

17. Simple picture - G is the most oxidizable base (highest HOMO)

18. Further borne out by transmission and tunneling estimate • Surprise: higher trans- • mission 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 )

19. Role of water • Stabilizes more highly conducting B-DNA structure • Screens DNA and reduces oxidation potentials allowing proximity of G-levels to Au Fermi energy

20. MutY DNA [4Fe-4S] Short Story II: electrons in DNA damage sensing for repair? JC Chin, DL Cox, RRP Singh Biophysical J, 2008

21. Relevance to biology? G-G ``hot spot’’ • 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

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

23. 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.

24. 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)

25. Theory 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

26. A little math for the MD/QM • Free energy perturbation: H() = (1-HMutY(++)-OxoG(+)+ HMutY(+++)-OxoG(0) • Free energy difference: GMD = ∫dH(integral from 0 to 1) • Reorganization energy:  = (1/2){HH • Combination of energy differences G= GMD,tot - GMD,in + GQM,in 

27. Estimation 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 • 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

28. 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

29. R149W mutation (kills MutY efficacy) • R is right on optimal electron transfer pathway-losing hydrogen bond to DNA hurts HAD • Estimate ketR149W/ketWT = 1/8

30. L154F mutation • More subtle - extra F size expands MutY and increases DA distance • Factor of 2 decrease in optimal rates

31. L154F mutation • More subtle - extra F size expands MutY and increases DA distance • Factor of 2 decrease in optimal rates

32. Conclusion • Preferential binding of MutY(3+) in vicinity Of oxidized oxoguanine • Enhanced Binding allows faster finding of damage site.

33. 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/0201404 SS Mallajosyula et al. PRL 101 176805 (2008) JC Lin, DL Cox, RRP Singh Biophys J. 95,3259 (2008)