SUPPORTING INFORMATION. The adaptive response enzyme AlkB preferentially repairs 1-methylguanine and. 3-methylthymine adducts in double-stranded DNA
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1 SUPPORTING INFORMATION The adaptive response enzyme AlkB preferentially repairs 1-methylguanine and 3-methylthymine adducts in double-stranded DNA Fangyi Chen, ± Qi Tang, ± Ke Bian, Zachary T. Humulock, Xuedong Yang, Marco Jost, Catherine L. Drennan, John M. Essigmann, Deyu Li* Corresponding Author * ± F.C. and Q.T. contributed equally to this work. S1
2 TABLE OF CONTENTS Table S1. Calculated and observed monoisotopic molecular weight and m/z value of oligonucleotides present in the enzyme repair reactions. Table S2. Repair efficiency of the three enzymes on four lesions. Each repair reaction was carried out in triplicate. Table S3. Enzyme concentrations of the three enzymes in the repair reactions. Table S4. Enzyme concentrations of AlkB in the reactions of measuring the initial velocity. Table S5. Repair efficiency of the AlkB enzyme on four lesions with additional 15μM unrelated 23mer DNA. Figure S1. Repair efficiency of ABH2 on different adducts in ss- and ds-dna. Figure S2. Repair efficiency of ABH3 on different adducts in ss- and ds-dna. Figure S3. Polyacrylamide gel electrophoresis of purified AlkB protein. Figure S4. Polyacrylamide gel electrophoresis of purified ABH2 protein. Figure S5. Polyacrylamide gel electrophoresis of purified ABH3 protein. Figure S6. Purity test of oligonucleotides containing the four alkyl adducts by HPLC. Figure S7. Purity test of oligonucleotides containing A/C/G/T in the 17mer complementary strands by HPLC. Figure S8. ESI-TOF analysis of 16mer oligonucleotide containing m1a. Figure S9. ESI-TOF analysis of 16mer oligonucleotide containing m3c. Figure S1. ESI-TOF analysis of 16mer oligonucleotide containing m1g. Figure S11. ESI-TOF analysis of 16mer oligonucleotide containing m3t. Figure S12. ESI-TOF analysis of 17mer oligonucleotide containing A. Figure S13. ESI-TOF analysis of 17mer oligonucleotide containing C. Figure S14. ESI-TOF analysis of 17mer oligonucleotide containing G. Figure S15. ESI-TOF analysis of 17mer oligonucleotide containing T. Figure S16. Repair efficiency of AlkB on different adducts in ss- and ds-dna with nonmutagenic pairing and additional 15μM unrelated 23mer DNA. S2
3 Table S1. Calculated and observed monoisotopic molecular weight and m/z value of oligonucleotides present in the enzyme repair reactions. The sequence of the 16mer oligos is 5 -GAAGACCTXGGCGTCC-3, where X indicates the position of the lesions and the repaired products. The sequence of the 17mer oligos is 5 - TGGACGCCYAGGTCTTC-3, where Y represents the position incorporating the complementary bases. Lesion or base MW (calculated) of neutral species m/z (calculate) -4 charge peak m/z (observed) -4 charge peak 16mer m1a mer m3c mer m1g mer m3t mer A mer C mer G mer T mer A mer C mer G mer T S3
4 Table S2. Repair efficiency of the three enzymes on four lesions (Figure 3). Each repair reaction was carried out in triplicate. AlkB repair of indicated lesion in ss-dna and ds-dna. Lesion Repair ratio in ss-dna and ds-dna (%) ss-dna lesion+a lesion+c lesion+g lesion+t m1a 53.4 ± ± ±.2.3 ± ± 1.4 m3c 79. ± ± ± ± ± 1.4 m1g 48.2 ± ± ± ± ±.5 m3t 12. ± ± ± ± ±.5 ABH2 repair of indicated lesion in ss-dna and ds-dna. Lesion Repair ratio in ss-dna and ds-dna (%) ss-dna lesion+a lesion+c lesion+g lesion+t m1a 64.5 ± ± ± ± ± 1.2 m3c 59.7 ± ± ± ± ±.3 m1g 22.2 ± ± ± ± ± 1.5 m3t 15.9 ± ± ± ± ±.8 ABH3 repair of indicated lesion in ss-dna and ds-dna. Lesion Repair ratio in ss-dna and ds-dna (%) ss-dna lesion+a lesion+c lesion+g lesion+t m1a 72. ± ± ± ± ±.5 m3c 57. ± ± ± ±.5.9 ±.2 S4
5 Table S3. Enzyme concentrations of the three enzymes in the repair reactions. For each repair reaction, 5 μm 16mer DNA oligo and the corresponding concentration of the enzyme in this table were used. * the repair efficiencies of ABH3 on m1g and m3t were extremely low and the products were undetectable even with addition of large excess amount of the enzyme, such as adding 5μM enzyme to 5μM DNA adducts. lesion AlkB (μm) ABH2 (μm) ABH3 (μm) m1a m3c m1g * m3t * Table S4. Enzyme concentrations of AlkB in the reactions of measuring the initial velocity. For each repair reaction, 5 μm 16mer DNA oligo and the corresponding concentration of AlkB in this table were used. Lesion AlkB (μm) m1a.1 m3c.35 m1g 2. m3t 1.5 Table S5. Repair efficiency of the AlkB enzyme on four lesions with additional 15μM unrelated 23mer DNA. The ds-dna reactions were carried out with the perfect match base pairs of each adduct. The corresponding concentrations of AlkB were listed in the table. Each repair reaction was carried out in triplicate. lesion ss-dna (%) ds-dna (%) p-value AlkB (μm) m1a 56.8 ± ± m3c 31.3 ± ± m1g.3 ± ± m3t 13.7± ±.8 < S5
6 1 ** 1 ** ** 8 ** 8 Figure S1. Repair efficiency of ABH2 on different adducts in ss- and ds-dna. The error bars represent the standard deviation from triplicate experiments. The significance of the difference between ss-dna and ds-dna with non-mutagenic pairing was tested using the Student s two-tailed t test. ** indicates p-value <.1. S6
7 1 8 ** m1a m1a+a m1a+c m1a+g m1a+t 1 8 ** m3c m3c+a m3c+c m3c+g m3c+t Figure S2. Repair efficiency of ABH3 on different adducts in ss- and ds-dna. The error bars represent the standard deviation from triplicate experiments. The significance of the difference between ss-dna and ds-dna with non-mutagenic pairing was tested using the Student s two-tailed t test. ** indicates p-value <.1. S7
8 Figure S3. Polyacrylamide gel electrophoresis of purified AlkB protein. S8
9 Figure S4. Polyacrylamide gel electrophoresis of purified ABH2 protein. S9
10 Figure S5. Polyacrylamide gel electrophoresis of purified ABH3 protein. S1
11 Figure S6. Purity test of oligonucleotides containing the four alkyl adducts by HPLC. The retention time of the oligos is around 5. min. For each test, 1pmol oligo was injected. From top to bottom, the sub-figures represent 16mer oligos containing m1a, m3c, m1g, and m3t. S11
12 Figure S7. Purity test of oligonucleotides containing A/C/G/T in the 17mer complementary strands by HPLC. The retention time of the oligo is around 5. min. For each test, 1pmol oligo was injected. From top to bottom, the sub-figures represent 17mer oligos containing A, C, G, and T. S12
13 Figure S8. ESI-TOF analysis of 16mer oligonucleotide containing m1a. Figure S9. ESI-TOF analysis of 16mer oligonucleotide containing m3c. S13
14 Figure S1. ESI-TOF analysis of 16mer oligonucleotide containing m1g. The peak at is from an impurity. The peak at is the monoisotopic peak of the 16mer containing m1g. Figure S11. ESI-TOF analysis of 16mer oligonucleotide containing m3t. S14
15 Figure S12. ESI-TOF analysis of 17mer oligonucleotide containing A. Figure S13. ESI-TOF analysis of 17mer oligonucleotide containing C. S15
16 Figure S14. ESI-TOF analysis of 17mer oligonucleotide containing G. Figure S15. ESI-TOF analysis of 17mer oligonucleotide containing T. S16
17 m1a + AlkB + 23mer m3c + AlkB + 23mer 8 ** 3 1 * ss-m1a ds-m1a ss-m3c ds-m3c m1g + AlkB + 23mer m3t + AlkB + 23mer 8 * ** ss-m1g ds-m1g ss-m3t ds-m3t Figure S16. Repair efficiency of AlkB on different adducts in ss- and perfect match ds-dna with non-mutagenic pairing and additional 15μM unrelated ss-23mer DNA. The error bars represent the standard deviation from triplicate experiments. The significance of the difference between ss-dna and ds-dna with non-mutagenic pairing was tested using the Student s two-tailed t test. * indicates p-value <.5 and ** indicates p-value <.1. S17
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