Chinese Journal of Magnetic Resonance ›› 2015, Vol. 32 ›› Issue (2): 150-162.doi: 10.11938/cjmr20150202
Previous Articles Next Articles
LIU Chang-dong，ZHU Guang
Received:2015-03-17
Revised:2015-05-10
Online:2015-06-05
Published:2015-06-05
About author:LIU Chang-dong(1979-), male, born in Heilongjiang, PhD., his research focuses on NMR.
*Corresponding author: ZHU Guang, Tel: +852-23588705, E-mail: gzhu@ust.hk.
CLC Number:
LIU Chang-dong，ZHU Guang. Quadruplex Nucleic Acid Structure Determination by Solution NMR[J]. Chinese Journal of Magnetic Resonance, 2015, 32(2): 150-162.
| [1] Adrian M, Heddi B, Phan A T. NMR spectroscopy of G-quadruplexes[J]. Methods. 2012, 57(1): 11－24.[2] Zhu G, Bax A. Improved linear prediction for truncated signals of known phase[J]. J Magn Reson, 1990, 90(2): 405－410.[3] Delaglio F, Grzesiek S, Vuister G W, et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes[J]. J Biomol NMR, 1995, 6(3): 277－293.[4] Vorlickova M, Kejnovska I, Sagi J, et al. Circular dichroism and guanine quadruplexes[J]. Methods, 2012, 57(1): 64－75.[5] Randazzo A, Spada G P, Da S M. Circular dichroism of quadruplex structures[J]. Top Curr Chem, 2013, 330: 67－86.[6] Karsisiotis A I, Hessari N M, Novellino E, et al. Topological characterization of nucleic acid G-quadruplexes by UV absorption and circular dichroism[J]. Angew Chem Int Ed Engl, 2011, 50(45): 10 645－10 648.[7] Paramasivan S, Rujan I, Bolton P H. Circular dichroism of quadruplex DNAs: applications to structure, cation effects and ligand binding[J]. Methods, 2007, 43(4): 324－331.[8] Feigon J, Koshlap K M, Smith F W. 1H NMR spectroscopy of DNA triplexes and quadruplexes[J]. Methods Enzymol, 1995, 261: 225－255.[9] Patel D J, Tonelli A E. Assignment of the proton Nmr chemical shifts of the T-N3H and G-N1H proton resonances in isolated AT and GC Watson-Crick base pairs in double-stranded deoxy oligonucleotides in aqueous solution[J]. Biopolymers, 1974, 13(10): 1 943－1 964.[10] Wuthrich K. NMR of Proteins and Nucleic Acid[M]. New York: John Wiley & Sons, 1986.[11] Wijmenga S S, Mooren M W, Hilbers C W. NMR of Nucleic Acids: from Spectrum to Structure[M]. Oxford: Oxford University Press, 1993.[12] Wijmenga S S, van Buuren B N M. The use of NMR methods for conformational studies of nucleic acids[J]. Prog Nucl Magn Reson Spectrosc, 1998, 32(4): 287－387.[13] Wang Y, Patel D J. Solution structure of the Oxytricha telomeric repeat d[G4(T4G4)3] G-tetraplex[J]. J Mol Biol, 1995, 251(1): 76－94.[14] Phan A T. Long-range imino proton-13C J-couplings and the through-bond correlation of imino and non-exchangeable protons in unlabeled DNA[J]. J Biomol NMR, 2000, 16(2): 175－178.[15] Phan A T, Patel D J. A site-specific low-enrichment 15N, 13C isotope-labeling approach to unambiguous NMR spectral assignments in nucleic acids[J]. J Am Chem Soc, 2002, 124(7): 1 160－1 161.[16] Martadinata H, Phan A T. Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution[J]. J Am Chem Soc, 2009, 131(7): 2 570－2 578.[17] Phan A T, Kuryavyi V, Darnell J C, et al. Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction[J]. Nat Struct Mol Biol, 2011, 18(7): 796－804.[18] Phan A T, Gueron M, Leroy J L. Investigation of unusual DNA motifs[J]. Methods Enzymol, 2001, 338: 341－371.[19] Dias E, Battiste J L, Williamson J R. Chemical probe for glycosidic conformation in telomeric DNAs[J]. J Am Chem Soc, 1994, 116(10): 4 479－4 480.[20] Clowney L, Jain S C, Srinivasan A R, et al. Geometric parameters in nucleic acids: nitrogenous bases[J]. J Am Chem Soc, 1996, 118(3): 509－518.[21] Gelbin A, Schneider B, Clowney L, et al. Geometric parameters in nucleic acids: sugar and phosphate constituents[J]. J Am Chem Soc, 1996, 118(3): 519－529.[22] Foloppe N, MacKerell A D Jr. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data[J]. J Comput Chem, 2000, 21(2): 86－104.[23] Schoeftner S, Blasco M A. Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II[J]. Nat Cell Biol, 2008, 10(2): 228－236.[24] Azzalin C M, Reichenbach P, Khoriauli L, et al. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends[J]. Science, 2007, 318(5 851): 798－801.[25] Horard B, Gilson E. Telomeric RNA enters the game[J]. Nat Cell Biol, 2008, 10(2): 113－115.[26] Joachimi A, Benz A, Hartig J S. A comparison of DNA and RNA quadruplex structures and stabilities[J]. Bioorg Med Chem, 2009, 17(19): 6 811－6 815.[27] Collie G W, Haider S M, Neidle S, et al. A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex[J]. Nucleic Acids Res, 2010, 38(16): 5 569－5 580.[28] Xu Y, Ishizuka T, Kimura T, et al. A U-tetrad stabilizes human telomeric RNA G-quadruplex structure[J]. J Am Chem Soc, 2010, 132(21): 7 231－7 233.[29] Arora A, Maiti S. Differential biophysical behavior of human telomeric RNA and DNA quadruplex[J]. J Phys Chem B, 2009, 113(30): 10 515－10 520.[30] Collie G W, Parkinson G N, Neidle S, et al. Electrospray mass spectrometry of telomeric RNA (TERRA) reveals the formation of stable multimeric G-quadruplex structures[J]. J Am Chem Soc, 2010, 132(27): 9 328－9 334.[31] Xu Y, Kaminaga K, Komiyama M. G-quadruplex formation by human telomeric repeats-containing RNA in Na+ solution[J]. J Am Chem Soc, 2008, 130(33): 11 179－11 184.[32] Phan A T. Human telomeric G-quadruplex: structures of DNA and RNA sequences[J]. FEBS J, 2010, 277(5): 1 107－1 117.[33] Zhang D H, Fujimoto T, Saxena S, et al. Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors[J]. Biochemistry, 2010, 49(21): 4 554－4 563.[34] Collie G W, Sparapani S, Parkinson G N, et al. Structural basis of telomeric RNA quadruplex--acridine ligand recognition[J]. J Am Chem Soc, 2011, 133(8): 2 721－2 728.[35] Martadinata H, Heddi B, Lim K W, et al. Structure of long human telomeric RNA (TERRA): G-quadruplexes formed by four and eight UUAGGG repeats are stable building blocks[J]. Biochemistry, 2011, 50(29): 6 455－6 461.[36] Randall A, Griffith J D. Structure of long telomeric RNA transcripts: the G-rich RNA forms a compact repeating structure containing G-quartets[J]. J Biol Chem, 2009, 284(21): 13 980－13 986.[37] Martadinata H, Phan A T. Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution[J]. J Am Chem Soc, 2009, 131(7): 2 570－2 578.[38] Xu Y, Suzuki Y, Ito K, et al. Telomeric repeat-containing RNA structure in living cells[J]. Proc Natl Acad Sci USA, 2010, 107(33): 14 579－14 584.[39] Biffi G, Tannahill D, Balasubramanian S. An intramolecular G-quadruplex structure is required for binding of telomeric repeat-containing RNA to the telomeric protein TRF2[J]. J Am Chem Soc, 2012, 134(29): 11 974－11 976.[40] Safa L, Delagoutte E, Petruseva I, et al. Binding polarity of RPA to telomeric sequences and influence of G-quadruplex stability[J]. Biochimie, 2014, 103: 80－88.[41] Ray S, Bandaria J N, Qureshi M H, et al. G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding[J]. Proc Natl Acad Sci USA, 2014, 111(8): 2 990－2 995.[42] Zaug A J, Podell E R, Cech T R. Human POT1 disrupts telomeric G-quadruplexes allowing telomerase extension in vitro[J]. Proc Natl Acad Sci USA, 2005, 102(31): 10 864－10 869.[43] Kelleher C, Kurth I, Lingner J. Human protection of telomeres 1 (POT1) is a negative regulator of telomerase activity in vitro[J]. Mol Cell Biol, 2005, 25(2): 808－818.[44] Ye J Z, Hockemeyer D, Krutchinsky A N, et al. POT1-interacting protein PIP1: a telomere length regulator that recruits POT1 to the TIN2/TRF1 complex[J]. Genes Dev, 2004, 18(14): 1 649－1 654.[45] Hwang H, Buncher N, Opresko P L, et al. POT1-TPP1 regulates telomeric overhang structural dynamics[J]. Structure, 2012, 20(11): 1 872－1 880.[46] Denchi E L, de Lange T. Protection of telomeres through independent control of ATM and ATR by TRF2 and POT1[J]. Nature, 2007, 448(7 157): 1 068－1 071.[47] Wang F, Podell E R, Zaug A J, et al. The POT1-TPP1 telomere complex is a telomerase processivity factor[J]. Nature, 2007, 445(7 127): 506－510.[48] Xiong J, Fan S, Meng Q, et al. BRCA1 inhibition of telomerase activity in cultured cells[J]. Mol Cell Biol, 2003, 23(23): 8 668－8 690.[49] Ballal R D, Saha T, Fan S, et al. BRCA1 localization to the telomere and its loss from the telomere in response to DNA damage[J]. J Biol Chem, 2009, 284(52): 36 083－36 098.[50] Scognamiglio P L, Di Natale C, Leone M, et al. G-quadruplex DNA recognition by nucleophosmin: new insights from protein dissection[J]. Biochim Biophys Acta, 2014, 1 840(6): 2 050－2 059.[51] Gonzalez V, Guo K, Hurley L, et al. Identification and characterization of nucleolin as a c-myc G-quadruplex-binding protein[J]. J Biol Chem, 2009, 284(35): 23 622－23 635.[52] Cogoi S, Zorzet S, Rapozzi V, et al. MAZ-binding G4-decoy with locked nucleic acid and twisted intercalating nucleic acid modifications suppresses KRAS in pancreatic cancer cells and delays tumor growth in mice[J]. Nucleic Acids Res, 2013, 41(7): 4 049－4 064.[53] Paramasivam M, Membrino A, Cogoi S, et al. Protein hnRNP A1 and its derivative Up1 unfold quadruplex DNA in the human KRAS promoter: implications for transcription[J]. Nucleic Acids Res, 2009, 37(9): 2 841－2 853. [54] Cogoi S, Paramasivam M, Membrino A, et al. The KRAS promoter responds to Myc-associated zinc finger and poly(ADP-ribose) polymerase 1 proteins, which recognize a critical quadruplex-forming GA-element[J]. J Biol Chem,2010, 285(29): 22 003－22 016.[55] De Cian A, Gros J, Guedin A, et al. DNA and RNA quadruplex ligands[J]. Nucleic Acids Symp Ser (Oxf), 2008, (52): 7－8.[56] Phan A T, Kuryavyi V, Gaw H Y, et al. Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter[J]. Nat Chem Biol, 2005, 1(3): 167－173.[57] Dai J, Carver M, Hurley L H, et al. Solution structure of a 2:1 quindoline-c-MYC G-quadruplex: insights into G-quadruplex-interactive small molecule drug design[J]. J Am Chem Soc, 2011, 133(44): 17 673－17 680.[58] Mayer M, Meyer B. Characterization of ligand binding by saturation transfer difference NMR spectroscopy[J]. Angew Chem Int Ed Engl, 1999, 28(12): 1 784－1 788.[59] Di Micco S, Bassarello C, Bifulco G, et al. Differential-frequency saturation transfer difference NMR spectroscopy allows the detection of different ligand-DNA binding modes[J]. Angew Chem Int Ed Engl, 2005, 45(2): 224－228.[60] Martino L, Virno A, Pagano B, et al. Structural and thermodynamic studies of the interaction of distamycin A with the parallel quadruplex structure [d(TGGGGT)]4[J]. J Am Chem Soc, 2007, 129(51): 16 048－16 056.[61] Zimmerman S B, Trach S O. Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli[J]. J Mol Biol, 1991, 222(3): 599－620.[62] Hansel R, Foldynova-Trantirkova S, Lohr F, et al. Evaluation of parameters critical for observing nucleic acids inside living Xenopus laevis oocytes by in-cell NMR spectroscopy[J]. J Am Chem Soc, 2009, 131(43): 15 761－15 768.[63] Hansel R, Lohr F, Foldynova-Trantirkova S, et al. The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions[J]. Nucleic Acids Res, 2011, 39(13): 5 768－5 775.[64] Hansel R, Lohr F, Trantirek L, et al. High-resolution insight into G-overhang architecture[J]. J Am Chem Soc, 2013, 135(7): 2 816－2 824.[65] Salgado G F, Cazenave C, Kerkour A, et al. G-quadruplex DNA and ligand interaction in living cells using NMR spectroscopy[J]. Chem Sci, 2015. DOI: 10.1039/C4SC03853C |
| [1] | CHI Xiu-juan, QIAO Xiao-ya, LIU Ying, LIU Hui-li, CHEN Lei, WANG Ji-hui, AI Xuan-jun. Purification of the AtGrp7 RRM Domain from Arabidopsis thaliana and Its Preliminary Structure and Binding Analysis [J]. Chinese Journal of Magnetic Resonance, 2019, 36(1): 1-14. |
| [2] | LI Hong-wei, YUAN Zhi-liang, XIA Bin. Determination of Apparent Protein Molecular Weight in Solution by Diffusion Ordered NMR Spectroscopy [J]. Chinese Journal of Magnetic Resonance, 2018, 35(3): 280-286. |
| [3] | SUN Wei-hang, SUN Yu, WANG Feng, WANG Chao-hong, YANG Tao. Optimization of Delays Alternating with Nutation for Tailored Excitation (DANTE) Sequence in Engineering [J]. Chinese Journal of Magnetic Resonance, 2018, 35(2): 150-161. |
| [4] | MA Er-qian, LI Yong-xiao, ZHAO Rui-ge, ZHANG Zhan-hui, YANG Qiu-qing. Interactions Between NP-10 and Single/Double Chain Quaternary Ammonium Salts Studied by NMR Spectroscopy [J]. Chinese Journal of Magnetic Resonance, 2017, 34(1): 16-24. |
| [5] | ZHOU Qiu-ju, XIANG Jun-feng, TANG Ya-lin, CUI Jie, WU Ning-ning. Pure Shift Proton NMR Spectroscopy and Its Applications [J]. Chinese Journal of Magnetic Resonance, 2016, 33(3): 502-513. |
| [6] | KUMAR Sriramoju M 1，LYU Ping-chiang1，HSU Shang-te Danny1,2,3*. Structural Perturbation of the Parkinson´s Disease-Associated I93M Mutation in Human UCH-L1 Revealed by Solution State NMR Spectroscopy [J]. Chinese Journal of Magnetic Resonance, 2015, 32(2): 329-341. |
| [7] | ZHANG Yan，ZHAO Bin，YANG Zhong-zheng，SHEN Jie，HU Wei，LAN Wen-xian，WU Hou-ming，CAO Chun-yang. Methods for Identification and Characterization of Protein Unexpectedly Expressed in Escherichia Coli: A Case Study Involving b-Lactamase Observed during the Expression of Zinc Finger 2-8 of NRSF/REST [J]. Chinese Journal of Magnetic Resonance, 2015, 32(1): 1-11. |
| [8] | LI Bo-jie，XU Jun*，WANG Qiang，WANG Xiu-mei，QI Guo-dong，DENG Feng*. Carbonylation of Methanol on Cu-H-MOR Zeolites: Insights from Solid-State NMR Spectroscopy [J]. Chinese Journal of Magnetic Resonance, 2014, 31(3): 331-340. |
| [9] | ZHANG Zheng-yang，QU Xiao-bo，LIN Yan-qin*，CHEN Zhong. A Sparse Reconstruction Algorithm for NMR Spectroscopy Based on Approximate l0 Norm Minimization [J]. Chinese Journal of Magnetic Resonance, 2013, 30(4): 528-540. |
| [10] | WANG Bei，LIU Xing，ZHU Guo-lei，LI Hai-zhou*. Applications of New Two-Dimensional NMR Spectroscopy in Natural Products Research [J]. Chinese Journal of Magnetic Resonance, 2013, 30(4): 602-613. |
| [11] | WEI Ying-liang*，MO Jian-guang，PAN Yan-kun. A Quantitative NMR Method for Period Verification of Sulfonamides Reference Materials [J]. Chinese Journal of Magnetic Resonance, 2013, 30(3): 371-379. |
| [12] | Sik Lok Lam. Overcoming the Challenges in Solution Structure Studies of CTG and CCTG Repeats [J]. Chinese Journal of Magnetic Resonance, 2012, 29(1): 1-20. |
| [13] | LI Hong-Yan, SZE Kong-Hung, FUNG King-Leung, SUN Gong-Zhe. Validation of Inter-Helical Orientation of the Sterile-α-Motif Domain of the Deleted in Liver Cancer 2 (DLC2-SAM) by 15N-1H Residual Dipolar Couplings [J]. Chinese Journal of Magnetic Resonance, 2010, 27(4): 584-596. |
| [14] | ZHOU Qiu-Ju, XIANG Jun-Feng, TANG Ya-Lin. Applications of Nuclear Magnetic Resonance Spectroscopy in Drug Discovery [J]. Chinese Journal of Magnetic Resonance, 2010, 27(1): 68-79. |
| [15] | SHA Yi; LI Wen; SHEN Hui-en. Determination of Clarithromycin Content by NMR [J]. Chinese Journal of Magnetic Resonance, 2009, 26(3): 308-315. |
| Viewed | ||||||
|
Full text |
|
|||||
|
Abstract |
|
|||||
