REFERENCES

1. Nitiss JL. Investigating the biological functions of DNA topoisomerases in eukaryotic cells. Biochim Biophys Acta 1998;1400:63-81.

2. Wang JC. Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 2002;3:430-40.

3. Nakasu S, Kikuchi A. Reverse gyrase; ATP-dependent Type I topoisomerase from Sulfolobus. EMBO J 1985;4:2705-10.

4. Tse-Dinh YC. Bacterial and archeal Type I topoisomerases. Biochim Biophys Acta 1998;1400:19-27.

5. Seki T, Seki M, Katada T, Enomoto T. Isolation of a cDNA encoding mouse DNA topoisomerase III which is highly expressed at the mRNA level in the testis. Biochim Biophys Acta 1998;1396:127-31.

6. Slesarev AI, Belova GI, Lake JA, Kozyavkin SA. Topoisomerase V from Methanopyrus kandleri. Methods Enzymol 2001;334:179-92.

7. Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A 1987;84:7024-7.

8. Sissi C, Palumbo M. Effects of magnesium and related divalent metal ions in topoisomerase structure and function. Nucleic Acids Res 2009;37:702-11.

9. Cuya SM, Bjornsti MA, van Waardenburg RCAM. DNA topoisomerase-targeting chemotherapeutics: what’s new? Cancer Chemother Pharmacol 2017;80:1-14.

10. Sekiguchi J, Shuman S. Site-specific ribonuclease activity of eukaryotic DNA topoisomerase I. Mol Cell 1997;1:89-97.

11. Champoux JJ. DNA topoisomerases: structure, function, and mechanism. Annu Rev Biochem 2001;70:369-413.

12. Pommier Y. Topoisomerase I inhibitors: camptothecins and beyond. Nat Rev Cancer 2006;6:789-802.

13. Champoux JJ. Domains of human topoisomerase I and associated functions. Prog Nucleic Acid Res Mol Biol 1998;60:111-32.

14. Stewart L, Ireton GC, Champoux JJ. Reconstitution of human topoisomerase I by fragment complementation. J Mol Biol 1997;269:355-72.

15. Redinbo MR, Stewart L, Champoux JJ, Hol WG. Structural flexibility in human topoisomerase I revealed in multiple non-isomorphous crystal structures. J Mol Biol 1999;292:685-96.

16. Stewart L, Redinbo MR, Qiu X, Hol WG, Champoux JJ. A model for the mechanism of human topoisomerase I. Science 1998;279:1534-41.

17. Wang Z, D’Annessa I, Tesauro C, Croce S, Ottaviani A, et al. Mutation of Gly717Phe in human topoisomerase 1B has an effect on enzymatic function, reactivity to the camptothecin anticancer drug and on the linker domain orientation. Biochim Biophys Acta 2015;1854:860-8.

18. Stewart L, Ireton GC, Champoux JJ. The domain organization of human topoisomerase I. J Biol Chem 1996;271:7602-8.

19. Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG. Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 1998;279:1504-13.

20. Redinbo MR, Champoux JJ, Hol WG. Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA. Biochemistry 2000;39:6832-40.

21. Laco GS, Pommier Y. Role of a tryptophan anchor in human topoisomerase I structure, function and inhibition. Biochem J 2008;411:523-30.

22. Albor A, Kaku S, Kulesz-Martin M. Wild-type and mutant forms of p53 activate human topoisomerase I: a possible mechanism for gain of function in mutants. Cancer Res 1998;58:2091-4.

23. Bharti AK, Olson MOJ, Kufe DW, Rubin EH. Identification of a nucleolin binding site in human topoisomerase I. J Biol Chem 1996;271:1993-7.

24. Simmons DT, Melendy T, Usher D, Stillman B. Simian virus 40 large T antigen binds to topoisomerase. Virology 1996;222:365-74.

25. Madden KR, Stewart L, Champoux JJ. Preferential binding of human topoisomerase I to superhelical DNA. EMBO J 1995;14:5399-409.

26. Schoeffler AJ, Berger JM. DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Q Rev Biophys 2008;41:41-101.

27. Woo MH, Losasso C, Guo H, Pattarello L, Benedetti P, et al. Locking the DNA topoisomerase I protein clamp inhibits DNA rotation and induces cell lethality. Proc Natl Acad Sci U S A 2003;100:13767-72.

28. Coletta A, Desideri A. Role of the protein in the DNA sequence specificity of the cleavage site stabilized by the camptothecin topoisomerase IB inhibitor: a metadynamics study. Nucleic Acids Res 2013;41:9977-86.

29. Siu FM, Pommier Y. Sequence selectivity of the cleavage sites induced by topoisomerase I inhibitors: a molecular dynamics study. Nucleic Acids Res 2013;41:10010-9.

30. Tesauro C, Morozzo della Rocca B, Ottaviani A, Coletta A, Zuccaro L, et al. Molecular mechanism of the camptothecin resistance of Glu710Gly topoisomerase IB mutant analyzed in vitro and in silico. Mol Cancer 2013;12:100.

31. D’Annessa I, Coletta A, Sutthibutpong T, Mitchell J, Chillemi G, et al. Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site. Nucleic Acids Res 2014;42:9304-12.

32. Sari L, Andricioaei I. Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation. Nucleic Acids Res 2005;33:6621-34.

33. Punchihewa C, Dai J, Carver M, Yang D. Human topoisomerase I C-terminal domain fragment containing the active site tyrosine is a molten globule: implication for the formation of competent productive complex. J Struct Biol 2007;159:111-21.

34. Cretaio E, Pattarello L, Fontebasso Y, Banedetti P, Losasso C. Human DNA topoisomerase IB: structure and functions. Ital J Biochem 2007;56:91-102.

35. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 2004;25:1605-12.

36. Tesauro C, Fiorani P, D’Annessa I, Chillemi G, Turchi G, et al. Erybraedin C, a natural compound from the plant Bituminaria bituminosa, inhibits both the cleavage and religation activities of human topoisomerase I. Biochem J 2010;425:531-9.

37. Arnò B, Coletta A, Tesauro C, Zuccaro L, Fiorani P, et al. A small organic compound enhances the religation reaction of human topoisomerase I and identifies crucial elements for the religation mechanism. Biosci Rep 2013;33:e00025.

38. Wu N, Wu XW, Agama K, Pommier Y, Du J, et al. A novel DNA topoisomerase I inhibitor with different mechanism from camptothecin induces G2/M phase cell cycle arrest to K562 cells. Biochemistry 2010;49:10131-6.

39. Ganguly A, Das B, Roy A, Sen N, Dasgupta SB, et al. Betulinic acid, a catalytic inhibitor of topoisomerase I, inhibits reactive oxygen species-mediated apoptotic topoisomerase I-DNA cleavable complex formation in prostate cancer cells but does not affect the process of cell death. Cancer Res 2007;67:11848-58.

40. Beretta GL, Gatti L, Perego P, Zaffaroni N. Camptothecin resistance in cancer: insights into the molecular mechanisms of a DNA-damaging drug. Curr Med Chem 2013;20:1541-65.

41. Li F, Jiang T, Li Q, Ling X. Camptothecin (CPT) and its derivatives are known to target topoisomerase I (Top1) as their mechanism of action: Did we miss something in CPT analogue molecular targets for treating human disease such as cancer? Am J Cancer Res 2017;7:2350-94.

42. Pizzolato JF, Saltz LB. Irinotecan (Campto®) in the treatment of pancreatic cancer. Expert Rev Anticancer Ther 2003;3:587-93.

43. Pizzolato JF, Saltz LB. The camptothecins. Lancet 2003;361:2235-42.

44. Horwitz MS, Horwitz SB. Intracellular degradation of HeLa and adenovirus type 2 DNA induced by camptothecin. Biochem Biophys Res Commun 1971;45:723-7.

45. Urasaki Y, Laco GS, Pourquier P, Takebayashi Y, Kohlhagen G, et al. Characterization of a novel topoisomerase I mutation from a camptothecin-resistant human prostate cancer cell line. Cancer Res 2001;61:1964-9.

46. Pommier Y. DNA topoisomerase I inhibitors: chemistry, biology, and interfacial inhibition. Chem Rev 2009;109:2894-902.

47. Lisby M, Olesen JR, Skouboe C, Krogh BO, Straub T, et al. Residues within the N-terminal domain of human topoisomerase I play a direct role in relaxation. J Biol Chem 2001;276:20220-7.

48. Fiorani P, Chillemi G, Losasso C, Castelli S, Desideri A. The different cleavage DNA sequence specificity explains the camptothecin resistance of the human topoisomerase I Glu418Lys mutant. Nucleic Acids Res 2006;34:5093-100.

49. Chrencik JE, Staker BL, Burgin AB, Pourquier P, Pommier Y, et al. Mechanisms of camptothecin resistance by human topoisomerase I mutations. J Mol Biol 2004;339:773-84.

50. Benedetti P, Fiorani P, Capuani L, Wang JC. Camptothecin resistance from a single mutation changing glycine 363 of human DNA topoisomerase I to cysteine. Cancer Res 1993;53:4343-8.

51. Fiorani P, Amatruda JF, Silvestri A, Butler RH, Bjornsti MA, et al. Domain interactions affecting human DNA topoisomerase I catalysis and camptothecin sensitivity. Mol Pharmacol 1999;56:1105-15.

52. D’Annessa I, Tesauro C, Wang Z, Arnò B, Zuccaro L, et al. The human topoisomerase 1B Arg634Ala mutation results in camptothecin resistance and loss of inter-domain motion correlation. Biochim Biophys Acta 2013;1834:2712-21.

53. D’Annessa I, Tesauro C, Fiorani P, Chillemi G, Castelli S, et al. Role of flexibility in protein-DNA-drug recognition: the case of Asp677Gly-Val703Ile topoisomerase mutant hypersensitive to camptothecin. J Amino Acids 2012;2012:206083.

54. Arnò B, D’Annessa I, Tesauro C, Zuccaro L, Ottaviani A, et al. Replacement of the human topoisomerase linker domain with the plasmodial counterpart renders the enzyme camptothecin resistant. PLoS One 2013;8:e68404.

55. Wright CM, Van Der Merwe M, DeBrot AH, Bjornsti MA. DNA topoisomerase I domain interactions impact enzyme activity and sensitivity to camptothecin. J Biol Chem 2015;290:12068-78.

56. Losasso C, Cretaio E, Fiorani P, D’Annessa I, Chillemi G, et al. A single mutation in the 729 residue modulates human DNA topoisomerase IB DNA binding and drug resistance. Nucleic Acids Res 2008;36:5635-44.

57. Pourquier P, Pommier Y. Topoisomerase I-mediated DNA damage. Adv Cancer Res 2001;80:189-216.

58. Fujimori A, Harker WG, Kohlhagen G, Hoki Y, Pommier Y. Mutation at the catalytic site of topoisomerase I in CEM/C2, a human leukemia cell line resistant to camptothecin. Cancer Res 1995;55:1339-46.