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NTIS 바로가기Nucleic acids research, v.49 no.17, 2021년, pp.10150 - 10165
Hur, Jeong Hwan (Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine , Suwon 16419, Republic of Korea) , Kang, Chan Young (Department of Chemistry, Hanyang University , Seoul 04763, Republic of Korea) , Lee, Sungjin (Department of Chemistry, Gwangju Institute of Science and Technology , Gwangju 61005, Republic of Korea) , Parveen, Nazia (Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine , Suwon 16419, Republic of Korea) , Yu, Jihyeon (Department of Chemistry, Hanyang University , Seoul 04763, Republic of Korea) , Shamim, Amen (Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), I) , Yoo, Wanki , Ghosh, Ambarnil , Bae, Sangsu , Park, Chin-Ju , Kim, Kyeong Kyu
AbstractI-motif or C4 is a four-stranded DNA structure with a protonated cytosine:cytosine base pair (C+:C) found in cytosine-rich sequences. We have found that oligodeoxynucleotides containing adenine and cytosine repeats form a stable secondary structure at a physiological pH with magnesium ion, w...
1. Crawford J.L. , Kolpak F.J. , Wang A.H. , Quigley G.J. , van Boom J.H. , van der Marel G. , Rich A. The tetramer d(CpGpCpG) crystallizes as a left-handed double helix . Proc. Natl. Acad. Sci. USA . 1980 ; 77 : 4016 – 4020 . 6933447
2. Conner B.N. , Takano T. , Tanaka S. , Itakura K. , Dickerson R.E. The molecular structure of d(ICpCpGpG), a fragment of right-handed double helical A-DNA . Nature . 1982 ; 295 : 294 – 299 . 7057893
3. Panayotatos N. , Wells R.D. Cruciform structures in supercoiled DNA . Nature . 1981 ; 289 : 466 – 470 . 7464915
4. Rhodes D. , Giraldo R. Telomere structure and function . Curr. Opin. Struct. Biol. 1995 ; 5 : 311 – 322 . 7583629
5. Leroy J.L. , Gueron M. , Mergny J.L. , Helene C. Intramolecular folding of a fragment of the cytosine-rich strand of telomeric DNA into an i-motif . Nucleic Acids Res. 1994 ; 22 : 1600 – 1606 . 8202359
6. Chakraborty S. , Sharma S. , Maiti P.K. , Krishnan Y. The poly dA helix: a new structural motif for high performance DNA-based molecular switches . Nucleic Acids Res. 2009 ; 37 : 2810 – 2817 . 19279188
7. Paeschke K. , Bochman M.L. , Garcia P.D. , Cejka P. , Friedman K.L. , Kowalczykowski S.C. , Zakian V.A. Pif1 family helicases suppress genome instability at G-quadruplex motifs . Nature . 2013 ; 497 : 458 – 462 . 23657261
8. Wolfl S. , Wittig B. , Rich A. Identification of transcriptionally induced Z-DNA segments in the human c-myc gene . Biochim. Biophys. Acta . 1995 ; 1264 : 294 – 302 . 8547317
9. Wittig B. , Wolfl S. , Dorbic T. , Vahrson W. , Rich A. Transcription of human c-myc in permeabilized nuclei is associated with formation of Z-DNA in three discrete regions of the gene . EMBO J. 1992 ; 11 : 4653 – 4663 . 1330542
10. Ambrus A. , Chen D. , Dai J. , Bialis T. , Jones R.A. , Yang D Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution . Nucleic Acids Res. 2006 ; 34 : 2723 – 2735 . 16714449
11. Sen D. , Gilbert W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis . Nature . 1988 ; 334 : 364 – 366 . 3393228
12. Siddiqui-Jain A. , Grand C.L. , Bearss D.J. , Hurley L.H. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription . Proc. Natl. Acad. Sci. USA . 2002 ; 99 : 11593 – 11598 . 12195017
13. Kaiser C.E. , Van Ert N.A. , Agrawal P. , Chawla R. , Yang D. , Hurley L.H. Insight into the complexity of the i-Motif and G-Quadruplex DNA structures formed in the KRAS promoter and subsequent drug-induced gene repression . J. Am. Chem. Soc. 2017 ; 139 : 8522 – 8536 . 28570076
14. Onel B. , Carver M. , Wu G. , Timonina D. , Kalarn S. , Larriva M. , Yang D A new G-Quadruplex with hairpin loop immediately upstream of the human BCL2 P1 promoter modulates transcription . J. Am. Chem. Soc. 2016 ; 138 : 2563 – 2570 . 26841249
15. Grand C.L. , Powell T.J. , Nagle R.B. , Bearss D.J. , Tye D. , Gleason-Guzman M. , Hurley L.H. Mutations in the G-quadruplex silencer element and their relationship to c-MYC overexpression, NM23 repression, and therapeutic rescue . Proc. Natl. Acad. Sci. USA . 2004 ; 101 : 6140 – 6145 . 15079086
16. Dhakal S. , Yu Z. , Konik R. , Cui Y. , Koirala D. , Mao H. G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA . Biophys. J. 2012 ; 102 : 2575 – 2584 . 22713573
17. Kang H.J. , Kendrick S. , Hecht S.M. , Hurley L.H. The transcriptional complex between the BCL2 i-motif and hnRNP LL is a molecular switch for control of gene expression that can be modulated by small molecules . J. Am. Chem. Soc. 2014 ; 136 : 4172 – 4185 . 24559432
18. Niu K. , Zhang X. , Deng H. , Wu F. , Ren Y. , Xiang H. , Zheng S. , Liu L. , Huang L. , Zeng B. et al . BmILF and i-motif structure are involved in transcriptional regulation of BmPOUM2 in Bombyx mori . Nucleic Acids Res. 2017 ; 46 : 1710 – 1723 .
19. Zeraati M. , Langley D.B. , Schofield P. , Moye A.L. , Rouet R. , Hughes W.E. , Bryan T.M. , Dinger M.E. , Christ D 2018) I-motif DNA structures are formed in the nuclei of human cells . Nat. Chem. 10 : 631 – 637 . 29686376
20. Gehring K. , Leroy J.L. , Gueron M. A tetrameric DNA structure with protonated cytosine.cytosine base pairs . Nature . 1993 ; 363 : 561 – 565 . 8389423
21. Sun D. , Hurley L.H. The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression . J. Med. Chem. 2009 ; 52 : 2863 – 2874 . 19385599
22. Rajendran A. , Nakano S. , Sugimoto N. Molecular crowding of the cosolutes induces an intramolecular i-motif structure of triplet repeat DNA oligomers at neutral pH . Chem. Commun. 2010 ; 46 : 1299 – 1301 .
23. Cantor C.R. , Warshaw M.M. , Shapiro H. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides . Biopolymers . 1970 ; 9 : 1059 – 1077 . 5449435
24. Sklenar V. , Bax A. Spin-echo water suppression for the generation of pure-phase two-dimensional NMR spectra . J. Magn. Reson . 1987 ; 74 : 469 – 479 .
25. Case D.C. , Cheatham T. , Darden T. , Duke R. , Giese T.J. , Gohlke H. , Götz A. , Greene D. , Homeyer N. , Izadi S. et al . Amber 2017 . 2017 ; San Francisco University of California .
26. Roe D.R. , Cheatham T.E. PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data . J. Chem. Theory Comput. 2013 ; 9 : 3084 – 3095 . 26583988
27. Vaught A. Graphing with Gnuplot and Xmgr: two graphing packages available under linux . Linux J. 1996 ; 1996 : 7 .
28. Jorgensen W. Transferable intermolecular potential functions for water, alcohols and ethers. Application to liquid water . J. Am. Chem. Soc. 1981 ; 103 : 335 – 340 .
29. Ryckaert J.P. , Ciccotti G. , Berendsen H.J. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes . J. Comput. Phys. 1977 ; 23 : 327 – 341 .
30. Berendsen H.J. , Postma J.V. , van Gunsteren W.F. , DiNola A.R.H.J. , Haak J.R. Molecular dynamics with coupling to an external bath . J. Chem. Phys. 1984 ; 81 : 3684 – 3690 .
31. Park J. , Lim K. , Kim J.S. , Bae S. Cas-analyzer: an online tool for assessing genome editing results using NGS data . Bioinformatics . 2017 ; 33 : 286 – 288 . 27559154
32. Tajmir-Riahi H.A. , Langlais M. , Savoie R. A laser Raman spectroscopic study of the interaction of calf-thymus DNA with Cu(II) and Pb(II) ions: metal ion binding and DNA conformational changes . Nucleic Acids Res. 1988 ; 16 : 751 – 762 . 3340554
33. Langlais M. , Tajmir-Riahi H.A. , Savoie R. Raman spectroscopic study of the effects of Ca2+, Mg2+, Zn2+, and Cd2+ ions on calf thymus DNA: binding sites and conformational changes . Biopolymers . 1990 ; 30 : 743 – 752 . 2275976
34. Saxena S. , Joshi S. , Shankaraswamy J. , Tyagi S. , Kukreti S. Magnesium and molecular crowding of the cosolutes stabilize the i-motif structure at physiological pH . Biopolymers . 2017 ; 107 : e23018 .
35. Dai J. , Hatzakis E. , Hurley L.H. , Yang D I-motif structures formed in the human c-MYC promoter are highly dynamic–insights into sequence redundancy and I-motif stability . PLoS One . 2010 ; 5 : e11647 . 20657837
36. Bhattacharya P.K. , Cha J. , Barton J.K. 1H NMR determination of base-pair lifetimes in oligonucleotides containing single base mismatches . Nucleic Acids Res. 2002 ; 30 : 4740 – 4750 . 12409465
37. Keller H. , Weickhmann A.K. , Bock T. , Wohnert J. Adenine protonation enables cyclic-di-GMP binding to cyclic-GAMP sensing riboswitches . RNA . 2018 ; 24 : 1390 – 1402 . 30006500
38. Phan A.T. , Leroy J.L. Intramolecular i-motif structures of telomeric DNA . J. Biomol. Struct. Dyn. 2000 ; 17 : 245 – 251 . 22607431
39. Boulard Y. , Cognet J.A. , Gabarro-Arpa J. , Le Bret M. , Carbonnaux C. , Fazakerley G.V. Solution structure of an oncogenic DNA duplex, the K-ras gene and the sequence containing a central C.A or A.G mismatch as a function of pH: nuclear magnetic resonance and molecular dynamics studies . J. Mol. Biol. 1995 ; 246 : 194 – 208 . 7853397
40. Ulrich E.L. , Akutsu H. , Doreleijers J.F. , Harano Y. , Ioannidis Y.E. , Lin J. , Livny M. , Mading S. , Maziuk D. , Miller Z. et al . BioMagResBank . Nucleic Acids Res. 2008 ; 36 : D402 – D408 . 17984079
41. Leroy J.L. , Gueron M. Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons . Structure . 1995 ; 3 : 101 – 120 . 7743125
42. Esmaili N. , Leroy J.L. i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats . Nucleic Acids Res. 2005 ; 33 : 213 – 224 . 15647504
43. Weil J. , Min T. , Yang C. , Wang S. , Sutherland C. , Sinha N. , Kang C. Stabilization of the i-motif by intramolecular adenine-adenine-thymine base triple in the structure of d(ACCCT) . Acta Crystallograph. Section D, Biol. Crystallogr. 1999 ; 55 : 422 – 429 .
44. Dreos R. , Ambrosini G. , Groux R. , Cavin Perier R. , Bucher P. The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms . Nucleic Acids Res. 2017 ; 45 : D51 – D55 . 27899657
45. Jaluria P. , Betenbaugh M. , Konstantopoulos K. , Shiloach J. Enhancement of cell proliferation in various mammalian cell lines by gene insertion of a cyclin-dependent kinase homolog . BMC Biotech. 2007 ; 7 : 71 .
46. Tang C.L. , Alexov E. , Pyle A.M. , Honig B. Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides . J. Mol. Biol. 2007 ; 366 : 1475 – 1496 . 17223134
47. Halder A. , Halder S. , Bhattacharyya D. , Mitra A. Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study . Phys. Chem. Chem. Phys. 2014 ; 16 : 18383 – 18396 . 25070186
48. Wolter A.C. , Weickhmann A.K. , Nasiri A.H. , Hantke K. , Ohlenschlager O. , Wunderlich C.H. , Kreutz C. , Duchardt-Ferner E. , Wohnert J. A stably protonated adenine nucleotide with a highly shifted pKa value stabilizes the tertiary structure of a GTP-Binding RNA aptamer . Angew. Chem. 2017 ; 56 : 401 – 404 . 27885761
49. Dzatko S. , Krafcikova M. , Hansel-Hertsch R. , Fessl T. , Fiala R. , Loja T. , Krafcik D. , Mergny J.L. , Foldynova-Trantirkova S. , Trantirek L. Evaluation of the stability of DNA i-Motifs in the Nuclei of Living Mammalian Cells . Angew. Chem. 2018 ; 57 : 2165 – 2169 . 29266664
50. Day H.A. , Huguin C. , Waller Z.A. Silver cations fold i-motif at neutral pH . Chem. Commun. 2013 ; 49 : 7696 – 7698 .
51. Gao J. , Berden G. , Rodgers M.T. , Oomens J. Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals . Phys. Chem. Chem. Phys. 2016 ; 18 : 7269 – 7277 . 26894838
52. Abdelhamid M.A. , Fabian L. , MacDonald C.J. , Cheesman M.R. , Gates A.J. , Waller Z.A. Redox-dependent control of i-Motif DNA structure using copper cations . Nucleic Acids Res. 2018 ; 46 : 5886 – 5893 . 29800233
53. Lipfert J. , Doniach S. , Das R. , Herschlag D Understanding nucleic acid-ion interactions . Annu. Rev. Biochem. 2014 ; 83 : 813 – 841 . 24606136
54. Takahashi S. , Sugimoto N. Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells . Chem. Soc. Rev. 2020 ; 49 : 8439 – 8468 . 33047751
55. Zettl T. , Shi X. , Bonilla S. , Sedlak S.M. , Lipfert J. , Herschlag D The structural ensemble of a Holliday junction determined by X-ray scattering interference . Nucleic Acids Res. 2020 ; 48 : 8090 – 8098 . 32597986
56. Shamim A. , Parveen N. , Subramani V.K. , Kim K.K. Molecular packing interaction in DNA crystals . Crystals . 2020 ; 19 : 1093 .
57. Tippana R. , Xiao W. , Myong S. G-quadruplex conformation and dynamics are determined by loop length and sequence . Nucleic Acids Res. 2014 ; 42 : 8106 – 8114 . 24920827
58. Pandey S. , Agarwala P. , Maiti S. Effect of loops and G-quartets on the stability of RNA G-quadruplexes . J. Phys. Chem. B . 2013 ; 117 : 6896 – 6905 . 23683360
59. Zhang A.Y. , Bugaut A. , Balasubramanian S. A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology . Biochemistry . 2011 ; 50 : 7251 – 7258 . 21744844
60. Miglietta G. , Cogoi S. , Pedersen E.B. , Xodo L.E. GC-elements controlling HRAS transcription form i-motif structures unfolded by heterogeneous ribonucleoprotein particle A1 . Sci. Rep. 2015 ; 5 : 18097 . 26674223
61. Shioda N. , Yabuki Y. , Yamaguchi K. , Onozato M. , Li Y. , Kurosawa K. , Tanabe H. , Okamoto N. , Era T. , Sugiyama H. et al . Targeting G-quadruplex DNA as cognitive function therapy for ATR-X syndrome . Nat. Med. 2018 ; 24 : 802 – 813 . 29785027
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