[1] Frenkel, K., Goldstein, M.S. and Teebor, G.W. (1981) Identification of the cis-Thymine Glycol Moiety in Chemically Oxidized and Gamma-Irradiated Deoxyribonucleic Acid by High-Pressure Liquid Chromatography Analysis. Biochemistry, 20, 7566-7571.
http://dx.doi.org/10.1021/bi00529a035
[2] Teebor, G., Cummings, A., Frenkel, K., Shaw, A., Voituriez, L. and Cadet, J. (1987) Quantitative Measurement of the Diastereoisomers of cis Thymidine Glycol in Gamma-Irradiated DNA. Free Radical Research Communications, 2, 303-309.
http://dx.doi.org/10.3109/10715768709065296
[3] Wallace, S.S. (2002) Biological Consequences of Free Radi-cal-Damaged DNA Bases. Free Radical Biology & Medicine, 33, 1-14.
http://dx.doi.org/10.1016/S0891-5849(02)00827-4
[4] Adelman, R., Saul, R.L. and Ames, B.N. (1988) Oxidative Damage to DNA: Relation to Species Metabolic Rate and Life Span. Proceedings of the National Academy of Sciences of the United States of America, 85, 2706-2708.
http://dx.doi.org/10.1073/pnas.85.8.2706
[5] Zuo, S., Boorstein, R.J. and Teebor, G.W. (1995) Oxidative Damage to 5-Methylcytosine in DNA. Nucleic Acids Research, 23, 3239-3243.
http://dx.doi.org/10.1093/nar/23.16.3239
[6] Cathcart, R., Schwiers, E., Saul, R.L. and Ames, B.N. (1984) Thymine Glycol and Thymidine Glycol in Human and Rat Urine: A Possible Assay for Oxidative DNA Damage. Pro-ceedings of the National Academy of Sciences of the United States of America, 81, 5633-5637.
http://dx.doi.org/10.1073/pnas.81.18.5633
[7] Their, R., Brüning, T., Kocher, K., Blaszkewicz, M., Makropoulos, V., Sundberg, A. and Bolt, H.M. (1999) Determination of Urinary Thymidine Glycol Using Affinity Chromatography, HPLC and Post-Column Reaction Detection: A Biomarker of Oxidative DNA Damage upon Kidney Transplantation. Archives of Toxicology, 73, 479-484.
http://dx.doi.org/10.1007/s002040050638
[8] Makropoulos, W., Kocher, K., Heintz, B., Schwarz, E.R., Mertens, P.R. and Stefanidis, I. (2000) Urinary Thymidine Glycol as a Biomarker for Oxidative Stress after Kidney Transplantation. Renal Failure, 22, 499-510.
http://dx.doi.org/10.1081/JDI-100100891
[9] Lowe, F.J., Luettich, K. and Gregg, E.O. (2013) Lung Cancer Biomarkers for the Assessment of Modified Risk Tobacco Products: An Oxidative Stress Perspective. Biomarkers, 18, 183-195.
http://dx.doi.org/10.3109/1354750X.2013.777116
[10] Brown, K.L., Adams, T., Jasti, V.P., Basu, A.K. and Stone, M.P. (2008) Interconversion of the cis-5R,6S- and trans- 5R,6R-Thymine Glycol Lesions in Duplex DNA. Journal of the American Chemical Society, 130, 11701-11710.
http://dx.doi.org/10.1021/ja8016544
[11] Basu, A.K., Loechler, E.L., Leadon, S.A. and Essigmann, J.M. (1989) Genetic Effects of Thymine Glycol: Site-Specific Mutagenesis and Molecular Modeling Studies. Journal of the American Chemical Society, 86, 7677-7681.
http://dx.doi.org/10.1073/pnas.86.20.7677
[12] Belousova, E.A., Maga, G., Fan, Y., Kubareva, E.A., Romanova, E.A., Lebedeva, N.A., Oretskaya, T.S. and Lavrik, O.I. (2010) DNA Polymerases Beta and Lambda Bypass Thymine Glycol in Gapped DNA Structures. Biochemistry, 49, 4695-4704.
http://dx.doi.org/10.1021/bi901792c
[13] Aller, P., Duclos, S., Wallace, S.S. and Doublie, S. (2011) A Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex. Journal of Molecular Biology, 412, 22-34.
http://dx.doi.org/10.1016/j.jmb.2011.07.007
[14] Dolinnaya, N.G., Kubareva, E.A., Romanova, E.A., Trikin, R.M. and Oretskaya, T.S. (2013) Thymidine Glycol: The Effect on DNA Molecular Structure and Enzymatic Processing. Biochimie, 95, 134-147.
http://dx.doi.org/10.1016/j.biochi.2012.09.008
[15] Yang, F., Romanova, E., Kubareva, E., Dolinnaya, N., Gajdos, V., Burenina, O., Fedotova, E., Ellis, J.S., Oretskaya, T., Hianik, T. and Thompson, M. (2009) Detection of DNA Damage: Effect of Thymidine Glycol Residues on the Thermodynamic, Substrate and Interfacial Acoustic Properties of Oligonucleotide Duplexes. The Analyst, 134, 41-51.
http://dx.doi.org/10.1039/B806604N
[16] Wan, F. and Lenardo, M.J. (2010) The Nuclear Signaling of NF-κB: Current Knowledge, New Insights, and Future Perspectives. Cell Research, 20, 24-33.
http://dx.doi.org/10.1038/cr.2009.137
[17] McCool, K.W. and Miyamoto, S. (2012) DNA Damage-Dependent NF-κB Activation: NEMO Turns Nuclear Signaling Inside Out. Immunological Reviews, 246, 311-326.
http://dx.doi.org/10.1111/j.1600-065X.2012.01101.x
[18] Gerondakis, S., Banerjee, A., Grigoriadis, G., Vasanthakumar, A., Gugasyan, R., Sidwell, T. and Grumont, R.J. (2012) NF-κB Subunit Specificity in Hemopoiesis. Immunological Reviews, 246, 272-285.
http://dx.doi.org/10.1111/j.1600-065X.2011.01090.x
[19] Mincheva-Tasheva, S. and Soler, R.M. (2013) NF-κB Signaling Pathways: Role in Nervous System Physiology and Pathology. Neuroscientist, 19, 175-194.
http://dx.doi.org/10.1177/1073858412444007
[20] Oh, H. and Ghosh, S. (2013) NF-κB: Roles and Regulation in Different CD4+ T-Cell Subsets. Immunological Reviews, 252, 41-51.
http://dx.doi.org/10.1111/imr.12033
[21] Niederberger, E. and Geisslinger, G. (2013) Proteomics and NF-κB: An Update. Expert Review of Proteomics, 10, 189-204.
http://dx.doi.org/10.1586/epr.13.5
[22] O’Dea, E. and Hoffmann, A. (2010) The Regulatory Logic of the NF-κB Signaling System. Cold Spring Harbor Perspectives in Biology, 2, a000216.
http://dx.doi.org/10.1101/cshperspect.a000216
[23] Ghosh, G., Wang, V.Y., Huang, D.B. and Fusco, A. (2012) NF-κB Regulation: Lessons from Structures. Immuno- logical Reviews, 246, 36-58.
http://dx.doi.org/10.1111/j.1600-065X.2012.01097.x
[24] Gilmore, T.D. (2006) Introduction to NF-κB: Players, Pathways, Perspectives. Oncogene, 25, 6680-6684.
http://dx.doi.org/10.1038/sj.onc.1209954
[25] Saccani, S., Pantano, S. and Natoli, G. (2003) Modulation of NF-κB Activity by Exchange of Dimers. Molecular Cell, 11, 1563-1574.
http://dx.doi.org/10.1016/S1097-2765(03)00227-2
[26] Kabe, Y., Ando, K., Hirao, S., Yoshida, M. and Handa, H. (2005) Redox Regulation of NF-κB Activation: Distinct Redox Regulation between the Cytoplasm and the Nucleus. Antioxidants & Redox Signaling, 7, 395-403.
http://dx.doi.org/10.1089/ars.2005.7.395
[27] Kunsch, C., Ruben, S.M. and Rosen, C.A. (1992) Selection of Optimal Κ-B/Rel DNA-Binding Motifs: Interaction of Both Subunits of NF-κB with DNA Is Required for Transcriptional Activation. Molecular and Cellular Biology, 12, 4412-4421.
http://dx.doi.org/10.1128/MCB.12.10.4412
[28] Tisne, C., Delepierre, M. and Hartmann, B. (1999) How NF-κB Can Be Attracted by Its Cognate DNA. Journal of Molecular Biology, 293, 139-150.
http://dx.doi.org/10.1006/jmbi.1999.3157
[29] Tisne, C., Hartmann, B. and Delepierre, M. (1999) NF-κ B Binding Mechanism: A Nuclear Magnetic Resonance and Modeling Study of a GGG → CTC Mutation. Biochemistry, 38, 3883-3894.
http://dx.doi.org/10.1021/bi982402d
[30] Wecker, K., Bonnet, M.C., Meurs, E.F. and Delepierre, M. (2002) The Role of the Phosphorus BI-BII Transition in Protein-DNA Recognition: The NF-κB Complex. Nucleic Acids Research, 30, 4452-4459.
http://dx.doi.org/10.1093/nar/gkf559
[31] Huang, D.B., Phelps, C.B., Fusco, A.J. and Ghosh, G. (2005) Crystal Structure of a Free κB DNA: Insights into DNA Recognition by Transcription Factor NF-κB. Journal of Molecular Biology, 346, 147-160.
http://dx.doi.org/10.1016/j.jmb.2004.11.042
[32] Hailer-Morrison, M.K., Kotler, J.M., Martin, B.D. and Sugden, K.D. (2003) Oxidized Guanine Lesions as Modulators of Gene Transcription. Altered p50 Binding Affinity and Repair Shielding by 7,8-Dihydro-8-oxo-2’-deoxyguanosine Lesions in the NF-κB Promoter Element. Biochemistry, 42, 9761-9770.
http://dx.doi.org/10.1021/bi034546k
[33] Karyagina, A., Shilov, I., Tashlitskii, V., Khodoun, M., Vasilev, S., Lau, P.C. and Nikolskaya, I. (1997) Specific Binding of SsoII DNA Methyltransferase to Its Promoter Region Provides the Regulation of SsoII Restriction-Modification Gene Expression. Nucleic Acids Research, 25, 2114-2120.
http://dx.doi.org/10.1093/nar/25.11.2114
[34] Shilov, I., Tashlitsky, V., Khodoun, M., Vasil’ev, S., Alekseev, Y., Kuzubov, A., Kubareva, E. and Karyagina, A. (1998) DNA-Methyltransferase SsoII Interaction with Own Promoter Region Binding Site. Nucleic Acids Research, 26, 2659-2664.
http://dx.doi.org/10.1093/nar/26.11.2659
[35] Konarev, P.V., Kachalova, G.S., Ryazanova, A.Y., Kubareva, E.A., Karyagina, A.S., Bartunik, H.D. and Svergun, D.I. (2014) Flexibility of the Linker between the Domains of DNA Methyltransferase SsoII Revealed by Small-Angle X-Ray Scattering: Implications for Transcription Regulation in SsoII Restriction-Modification System. PLoS ONE, 9, e93453.
http://dx.doi.org/10.1371/journal.pone.0093453
[36] Smith, D.B. and Johnson, K.S. (1988) Single-Step Purification of Polypeptides Expressed in Escherichia coli as Fusions with Glutathione S-Transferase. Gene, 67, 31-40.
http://dx.doi.org/10.1016/0378-1119(88)90005-4
[37] Tanaka, H., Vickart, P., Bertrand, J.R., Rayner, B., Morvan, F., Imbach, J.L., Paulin, D. and Malvy, C. (1994) Sequence-Specific Interaction of Alpha-Beta-Anomeric Double-Stranded DNA with the p50 Subunit of NFκB: Application to the Decoy Approach. Nucleic Acids Research, 22, 3069-3074.
http://dx.doi.org/10.1093/nar/22.15.3069
[38] Thi, H.L., Zatsepin T.S., Schierling B., Volkov, E.M., Wende, W., Pingoud, A., Kubareva, E.A. and Oretskaya T.S. (2011) Restriction Endonuclease SsoII with Photoregulated Activity — A “Molecular Gate” Approach. Bioconjugate Chemistry, 22, 1366-1373.
http://dx.doi.org/10.1021/bc200063m
[39] Ryazanova, A.Y., Winkler, I., Friedhoff, P., Viryasov, M.B., Oretskaya, T.S. and Kubareva, E.A. (2011) Crosslinking of (Cytosine-5)-DNA Methyltransferase SsoII and Its Complexes with Specific DNA Duplexes Provides an Insight into Their Structures. Nucleosides Nucleotides & Nucleic Acids, 30, 632-650.
http://dx.doi.org/10.1080/15257770.2011.584339
[40] Cantor, C.R., Warshaw, M.M. and Shapiro, H. (1970) Oligonucleotide Interactions. 3. Circular Dichroism Studies of the Conformation of Deoxyoligonucleotides. Biopolymers, 9, 1059-1077.
http://dx.doi.org/10.1002/bip.1970.360090909
[41] Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham III, T.E., Laughton, C.A. and Orozco, M. (2007) Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of Alpha/Gamma Conformers. Biophysical Journal, 92, 3817-3829.
http://dx.doi.org/10.1529/biophysj.106.097782
[42] Dupradeau, F.Y., Pigache, A., Zaffran, T., Savineau, C., Lelong, R., Grivel, N., Lelong, D., Rosanski, W. and Cieplak, P. (2010) The R.E.D. Tools: Advances in RESP and ESP Charge Derivation and Force Field Library Building. Physical Chemistry Chemical Physics, 12, 7821-7839.
http://dx.doi.org/10.1039/c0cp00111b
[43] Gordon, M.S. and Schmidt, M.W. (2005) Advances in Electronic Structure Theory: GAMESS a Decade Later. In: Dykstra, C.E., Frenking, G., Kim, K.S. and Scuseria, G.E., Eds., Theory and Applications of Computational Chemistry: The First Forty Years, Elsevier, Amsterdam, 1167-1189.
http://dx.doi.org/10.1016/b978-044451719-7/50084-6
[44] Vorob’eva, O.V., Kariagina, A.S., Volkov, E.M., Viriasov, M.B., Oretskaia, T.S. and Kubareva, E.A. (2002) An Analysis of Methyltransferase SsoII-DNA Contacts in the Enzyme-Substrate Complex. Bioorganicheskaya Khimiya, 28, 402-410.
[45] Ryazanova, A.Y., Kubareva, E.A., Grman, I., Lavrova, N.V., Ryazanova, E.M., Oretskaya, T.S. and Hianik, T. (2011) The Study of the Interaction of (Cytosine-5)-DNA Methyltransferase SsoII with DNA by Acoustic Method. The Analyst, 136, 1227-1233.
http://dx.doi.org/10.1039/c0an00545b
[46] Scatchard, G. (1949) The Attractions of Proteins for Small Molecules an Ions. Annals of the New York Academy of Sciences, 51, 660-672.
http://dx.doi.org/10.1111/j.1749-6632.1949.tb27297.x
[47] Uporova, T.M., Kartashova, I.M., Skripkin, E.A., Lopareva, E. and Nikol’skaia, I.I. (1985) Restriction Endonucleases from Shigella sonnei 47. Voprosy Meditsinskoi Khimii, 31, 131-136.
[48] Kung, H.C. and Bolton, P.H. (1997) Structure of a Duplex DNA Containing a Thymine Glycol Residue in Solution. The Journal of Biological Chemistry, 272, 9227-9236.
http://dx.doi.org/10.1074/jbc.272.14.9227
[49] Brown, K.L., Roginskaya, M., Zou, Y., Altamirano, A., Basu, A.K. and Stone, M.P. (2010) Binding of the Human Nucleotide Excision Repair Proteins XPA and XPC/HR23B to the 5R-Thymine Glycol Lesion and Structure of the cis-(5R,6S) Thymine Glycol Epimer in the 5'-GTgG-3' Sequence: Destabilization of Two Base Pairs at the Lesion Site. Nucleic Acids Research, 38, 428-440.
http://dx.doi.org/10.1093/nar/gkp844
[50] Siggers, T., Chang, A.B., Teixeira, A., Wong, D., Williams, K.J., Ahmed, B., Ragoussis, J., Udalova, I.A., Smale, S.T. and Bulyk, M.L. (2012) Principles of Dimer-Specific Gene Regulation Revealed by a Comprehensive Characterization of NF-κB Family DNA Binding. Nature Immunology, 13, 95-102.
http://dx.doi.org/10.1038/ni.2151
[51] Metelev, V.G., Kubareva, E.A. and Oretskaya, T.S. (2013) Regulation of Activity of Transcription Factor NF-κB by Synthetic Oligonucleotides. Biochemistry (Moscow), 78, 867-878.
http://dx.doi.org/10.1134/s0006297913080026
[52] Sakurai, H., Chiba, H., Miyoshi, H., Sugita, T. and Toriumi, W. (1999) IκB Kinases Phosphorylate NF-κB p65 Subunit on Serine 536 in the Transactivation Domain. The Journal of Biological Chemistry, 274, 30353-30356.
http://dx.doi.org/10.1074/jbc.274.43.30353
[53] Yu, Z., Zhang, W. and Kone, B.C. (2002) Histone Deacetylases Augment Cytokine Induction of the iNOS Gene. Journal of the American Society of Nephrology, 13, 2009-2017.
http://dx.doi.org/10.1097/01.ASN.0000024253.59665.F1
[54] Schwabe, R.F., Schnabl, B., Kweon, Y.O. and Brenner, D.A. (2001) CD40 Activates NF-κB and c-Jun N-Terminal Kinase and Enhances Chemokine Secretion on Activated Human Hepatic Stellate Cells. Journal of Immunology, 166, 6812-6819.
http://dx.doi.org/10.4049/jimmunol.166.11.6812
[55] Benezra, M., Chevallier, N., Morrison, D.J., MacLachlan, T.K., El-Deiry, W.S. and Licht, J.D. (2003) BRCA1 Augments Transcription by the NF-κB Transcription Factor by Binding to the Rel Domain of the p65/RelA Subunit. The Journal of Biological Chemistry, 278, 26333-26341.
http://dx.doi.org/10.1074/jbc.M303076200
[56] Schwabe, R.F. and Sakurai, H. (2005) IKKbeta Phosphorylates p65 at S468 in Transactivaton Domain 2. FASEB Journal, 19, 1758-1760.
[57] Buss, H., Handschick, K., Jurrmann, N., Pekkonen, P., Beuerlein, K., Muller, H., Wait, R., Saklatvala, J., Ojala, P.M., Schmitz, M.L., Naumann, M. and Kracht, M. (2012) Cyclin-Dependent Kinase 6 Phosphorylates NF-κB P65 at Serine 536 and Contributes to the Regulation of Inflammatory Gene Expression. PLoS ONE, 7, e51847.
http://dx.doi.org/10.1371/journal.pone.0051847
[58] Ferguson, K.A. (1964) Starch-Gel Electrophoresis-Application to the Classification of Pituitary Proteins and Polypeptides. Metabolism, 13, 985-1002.
http://dx.doi.org/10.1016/S0026-0495(64)80018-4
[59] Muller, C.W., Rey, F.A., Sodeoka, M., Verdine, G.L. and Harrison, S.C. (1995) Structure of the NF-κB p50 Homodimer Bound to DNA. Nature, 373, 311-317.
http://dx.doi.org/10.1038/373311a0
[60] Ghosh, G., van Duyne, G., Ghosh, S. and Sigler, P.B. (1995) Structure of NF-κB p50 Homodimer Bound to a κB Site. Nature, 373, 303-310.
http://dx.doi.org/10.1038/373303a0
[61] Chen, Y.Q., Ghosh, S. and Ghosh, G. (1998) A Novel DNA Recognition Mode by the NF-κB p65 Homodimer. Nature Structural Biology, 5, 67-73.
http://dx.doi.org/10.1038/nsb0198-67
[62] Sengchanthalangsy, L.L., Datta, S., Huang, D.B., Anderson, E., Braswell, E.H. and Ghosh, G. (1999) Characterization of the Dimer Interface of Transcription Factor NFκB p50 Homodimer. Journal of Molecular Biology, 289, 1029-1040.
http://dx.doi.org/10.1006/jmbi.1999.2823
[63] Wurster, S.E., Bida, J.P., Her, Y.F. and Maher III, L.J. (2009) Characterization of Anti-NF-κB RNA Aptamer-Binding Specificity in Vitro and in the Yeast Three-Hybrid System. Nucleic Acids Research, 37, 6214-6224.
http://dx.doi.org/10.1093/nar/gkp670
[64] McTigue, M.A., Williams, D.R. and Tainer, J.A. (1995) Crystal Structures of a Schistosomal Drug and Vaccine Target: Glutathione S-Transferase from Schistosoma japonica and Its Complex with the Leading Antischistosomal Drug Praziquantel. Journal of Molecular Biology, 246, 21-27.
http://dx.doi.org/10.1006/jmbi.1994.0061
[65] Sheehan, D., Meade, G., Foley, V.M. and Dowd, C.A. (2001) Structure, Function and Evolution of Glutathione Transferases: Implications for Classification of Non-Mammalian Members of an Ancient Enzyme Superfamily. The Bio- chemical Journal, 360, 1-16.
http://dx.doi.org/10.1042/bj3600001
[66] Romanenkov, A.S., Ustyugov, A.A., Zatsepin, T.S., Nikulova, A.A., Kolesnikov, I.V., Metelev, V.G., Nikulova, A.A., Kolesnikov, I.V., Metelev, V.G., Oretskaya, T.S. and Kubareva, E.A. (2005) Analysis of DNA-Protein Interactions in Complexes of Transcription Factor NF-κB with DNA. Biochemistry (Moscow), 70, 1212-1222.
http://dx.doi.org/10.1007/s10541-005-0249-2
[67] Smale, S.T. (2012) Dimer-Specific Regulatory Mechanisms within the NF-κB Family of Transcription Factors. Immunological Reviews, 246, 193-204.
http://dx.doi.org/10.1111/j.1600-065X.2011.01091.x
[68] Hayden, M.S. and Ghosh, S. (2008) Shared Principles in NF-κB Signaling. Cell, 132, 344-362.
http://dx.doi.org/10.1016/j.cell.2008.01.020
[69] Nikolskaya, I.I., Lopatina, N.G., Suchkov, S.V., Kartashova, I.M. and Debov, S.S. (1984) Sequence Specificity of Isolated DNA-Cytosine Methylases from Shigella sonnei 47 Cells. Biochemistry International, 9, 771-781.
[70] Vorob’eva, O.V., Vasil’ev, S.A., Kariagina, A.S., Oretskaia, T.S. and Kubareva, E.A. (2000) Analysis of Contacts between DNA and Protein in a Complex of SsoII Methyltransferase-Promoter Region of the Gene for the SsoII Restriction-Modification System. Molekuliarnaia Biologiia, 34, 1074-1080.
[71] Romanenkov, A.S., Kisil, O.V., Zatsepin, T.S., Yamskova, O.V., Karyagina, A.S., Metelev, V.G., Oretskaia, T.S. and Kubareva, E.A. (2006) DNA-Methyltransferase SsoII as a Bifunctional Protein: Features of the Interaction with the Promoter Region of SsoII Restriction-Modification Genes. Biochemistry (Moscow), 71, 1341-1349.
http://dx.doi.org/10.1134/s0006297906120091