Cover sheet: Title: Inhibition of free DNA degradation by the deformation of DNA exposed to trace polymeric aromatic hydrocarbon contaminants

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1 Cover sheet: Title: Inhibition of free DNA degradation by the deformation of DNA exposed to trace polymeric aromatic hydrocarbon contaminants Authors: Fuxing Kang, Yanzheng Gao*, Wanting Ling, Qian Wang Number of pages: 9 Number of figures: 0 Number of tables: 3 Number of complementary Materials and Methods: 2 Number of references: 20 1

2 Tables: Table S1: Molecular structures and physicochemical properties of phenanthrene and pyrene used in this work (references 1, 2, 3, 4) Table S2: The adsorption bands of DNA from FTIR spectrum and their corresponding functional groups Table S3. The adsorption bands of DNase I enzyme from FTIR spectrum and their corresponding functional groups Materials and Methods: a. Rate of DNA Degradation by DNase I b. Processes of Treating FTIR Samples 2

3 Table S1. Molecular structures and physicochemical properties of phenanthrene and pyrene used in this work (references 1, 2, 3, 4) PAHs Molecular Structures Molecular Weight Solubility (µg L ) Purity LogK ow Phenanthrene % 4.45 Pyrene %

4 Table S2. The adsorption bands of DNA from FTIR spectrum and their corresponding functional groups Adsorption bands (cm -1 ) Functional groups References 970 ~ DNA backbone or asymmetric PO DNA backbone 6, Furanose vibration 8, Stretch vibration of P-O or C-O 10, Symmetrical stretch vibration of phosphate functional groups 6, Cytosine Guanine 6, CH 3 - Symmetric deformation deoxyribose thymine 11, 13, 14, and 1488 DNA structure 11, 13, 14, Imidazole ring 16, Stretch of C=C or C=N in base 16, thymine In-plane ring vibration of thymine Guanine carbonyl vibration 8, 9, 16, 18 4

5 Table S3. The adsorption bands of DNase I enzyme from FTIR spectrum and their corresponding functional groups Wave numbers (cm -1 ) Functional groups References amide I (C(N)=O) of α-helix of DNase I 18, and 1455 amide II (C-N+N-H) 18, amide III (N H bending and C N stretching vibrations) 19, unsaturated bands 19 5

6 Materials and Methods a. Rate of DNA Degradation by DNase I As for the dilute solution, the relationship between the absorbance (A 0 ) and the concentrations of absorbent substance (C) were defined by the following equation: A = k C, (1) 0 where k represents the absorption constant. And the concentration of absorbent substance could be obtained as follows: C = k / A 0. (2) As for the multiple absorbent substances composed of C 1, C 2, C 3 + C n, the equation (1) could be expressed as follows: A 0 k (C 1+C 2+C 3+...C n) =. (3) The concentration of multiple absorbent substances was expressed as: C + C + C +...C n 0 = k / A. (4) The varying quantity of DNA at any moment was expressed as: + = = δ. (5) f ( t δ ) f ( t ) (C 1' +C 2' +C 3' +...C n' ) (C 1+C 2+C C n) A 0 / k Therefore, the rate of DNA degradation was described as follows: v ( t ) (C +C +C +...C ) (C +C +C +...+C ) A ( ) = = = = (6) f ( t + δ ) f ( t) 1' 2' 3' n' n δ 0 df t lim lim lim δ 0 δ δ 0 δ δ 0 δ k dt where the (C 1'+C 2'+C 3'+...C n') was the absorbance of multiple absorbent substances for a specific wavelength at t +δ hour. As for the single absorbent substance, the varying rate of DNA degradation can be described as follows: v ( t ) f ( t + δ ) f ( t ) C ' C δ A 0 d f ( t ) = lim = lim = lim = (7) δ 0 δ δ 0 δ δ 0 δ k d t 6

7 where C and C represent the absorbance at t +δ and t moment, respectively. b. Processes of Treating FTIR Samples FTIR spectrum was employed to explore the changes in structures and bases of the DNA, DNA-PAHs, and DNase I. The DNA and DNase I solutions and the products of DNA degraded by DNase I after PAHs exposure were completely dried by vacuum freezing and drying equipment ( , Labconco ). The dried samples were mixed with the fine granular KBr, and the disc-formed samples were subjected to infrared to determine their configurations using a Nicolet FTIR spectrometer (Impact 420 model). 7

8 References 1. Gao, Y. Z.; Xiong, W.; Ling, W. T.; Wang, H., Ren, L. L.; Yang, Z. Y. Partitioning of polycyclic aromatic hydrocarbons between plant roots and water. Plant Soil 2008, 311, Gao, Y.Z.; Collins, C.D. Uptake pathways of polycyclic aromatic hydrocarbons in white clover. Environ. Sci. Technol. 2009, 43, Gao, Y. Z.; Shen, Q.; Ling, W. T.; Ren L. L. Uptake of polycyclic aromatic hydrocarbons by Trifolium pretense L. from water in the presence of a nonionic surfactant. Chemosphere 2008, 72, Gao, Y. Z.; Xiong, W.; Ling, W. T.; Wang, X. R.; Li, Q. L. Impact of exotic and inherent dissolved organic matter on sorption of phenanthrene by soils. J. Hazard. Mater. 2007, 140, Mao, Y.; Daniel Lambert, N.; Whittaker, N.; Saffiotti, U. DNA binding to crystalline silica characterized by Fourier-transform infrared spectroscopy. Environ. Health Persp. 1994, 102, Cai, P.; Huang, Q. Y.; Zhang, X. W. Interactions of DNA with clay minerals and soil colloidal particles and protection against degradation by DNase. Environ. Sci. Technol. 2007, 40, Liquier, J.; Taillandier, E. Infrared spectroscopy of nucleic acids, in: H.H. Mantsch, D. Chapman (Eds.), Infrared Spectroscopy of Biomolecules, Wiley-Liss, Inc, New York, Ouameur, A. A.; Tajmir-Riahi, H. A. Structural analysis of DNA interactions with biogenic polyamines and cobalt(iii)hexamine studied by Fourier transform infrared and capillary electrophoresis. J. Biol. Chem. 2004, 279, Loprete, M.; Hartman, K. A. Conditions for the stability of the B, C and Z structural forms of poly(dg-dc) in the presence of lithium, potassium, magnesium, calcium and zinc cations. Biochem. 1993, 32,

9 10. Shimanouchi, T.; Tsuboi, M.; Kyogoku, Y. Infrared spectra of nucleic acids and related compounds, in: J. Duchesne (Ed.), the structure and properties of biomolecules and biological systems, advances in chemical physics, Interscience, London, Alex, S.; Dupuis, P. FTIR and Raman investigation of cadmium binding by DNA. Inorg. Chim. Acta. 1986, 157, Tsuboi, M. Application of infrared spectroscopy to structure studies of nucleic acids, Applied Spectroscopy Reviews, in: E.G.J. Brame (Ed.), Dekker, New York, Taillandier, E.; Liquier, J. Infrared spectroscopy of DNA, Methods Enzymol. 1992, 211, Tajmir-Riahi, H. A.; Neault, J. F.; Naoui, M. Does DNA acid fixation produce left-handed Z structure? FEBS Lett. 1995, 370, Lindqvist, M. M.; Graslund, A. A. An FTIR and CD study of the structural effects of G-tract length and sequence context on DNA conformation in solution. J. Mol. Biol. 2001, 314, Banyay, M.; Gräslund, A. Structural effects of cytosine methylation on DNA surgar pucker studied by FTIR. J. Mol. Biol. 2002, 324, Taillandier, E.; Peticolas, W. L.; Adam, S.; Huynh-Dinh, T.; Igolen, J. Polymorphism of the d(cccgcggg)2 double helix studies by FTIR spectroscopy, Spectrochim. Acta. A. 1990, 46A, Tajmir-Riahi, H. A.; N soukpoé-kossi, C. N.; Joly, D. Structural analysis of protein-dna and protein-rna interactions by FTIR, UV-visible and CD spectroscopic methods. Spectroscopy 2009, 23, Haris, P. I.; Severcan, F. FTIR spectroscopic characterization of protein structure in aqueous and non-aqueous media. J. Molec. Catal. B: Enzymatic, 1999, 7: Andreoni, V.; Cavalca, L.; Rao, M. A.; Nocerino, G.; Bernasconi, S.; Dell Amico, E.; Colombo, M.; Gianfreda, L. Bacterial communities and enzyme activities of PAHs polluted soils. 9

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