Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom

doi:10.1007/s11705-016-1565-3

Frontiers of Chemical Science and Engineering

2016, Vol. 10

Issue (2): 196-202 https://doi.org/10.1007/s11705-016-1565-3

本期目录

Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom

Wen Zhang^1,^2,³,Jack W. Szostak²,Zhen Huang^1,^3,^*(

)

¹. Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
². Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
³. College of Life Sciences, Sichuan University, Chengdu 610041, China

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Abstract：

X-ray crystallography is a powerful strategy for 3-D structure determination of macromolecules, such as nucleic acids and protein-nucleic acid complexes. However, the crystallization and phase determination are the major bottle-neck problems in crystallography. Recently we have successfully developed synthesis and strategy of selenium-derivatized nucleic acids (SeNA) for nucleic acid crystallography. SeNA might not only provide the rational strategies to solve the phase determination problem, but also offer a potential strategy to explore crystallization solutions.

Key words： selenium DNA RNA nucleic acid crystallization

收稿日期: 2015-12-03 出版日期: 2016-05-19

Corresponding Author(s): Zhen Huang

引用本文:

. [J]. Frontiers of Chemical Science and Engineering, 2016, 10(2): 196-202.
Wen Zhang,Jack W. Szostak,Zhen Huang. Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom. Front. Chem. Sci. Eng., 2016, 10(2): 196-202.

链接本文:

https://academic.hep.com.cn/fcse/CN/10.1007/s11705-016-1565-3
https://academic.hep.com.cn/fcse/CN/Y2016/V10/I2/196

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1	Eddy S R. Non-coding RNA genes and the modern RNA world. Nature Reviews. Genetics, 2001, 2(12): 919–929 https://doi.org/10.1038/35103511
2	Blount K F, Uhlenbeck O C. The structure-function dilemma of the hammerhead ribozyme. Annual Review of Biophysics and Biomolecular Structure, 2005, 34(1): 415–440 https://doi.org/10.1146/annurev.biophys.34.122004.184428
3	Watson J D, Crick F H. Molecular structure of nucleic acids. Nature, 1953, 171(4356): 737–738 https://doi.org/10.1038/171737a0
4	Doherty E A, Doudna J A. Ribozyme structures and mechanisms. Annual Review of Biophysics and Biomolecular Structure, 2001, 30(1): 457–475 https://doi.org/10.1146/annurev.biophys.30.1.457
5	Shu Y, Pi F, Sharma A, Rajabi M, Haque F, Shu D, Leggas M, Evers B M, Guo P. Stable RNA nanoparticles as potential new generation drugs for cancer therapy. Advanced Drug Delivery Reviews, 2014, 66: 74–89 https://doi.org/10.1016/j.addr.2013.11.006
6	Zhang W, Huang Z. Synthesis of the 5′-se-thymidine phosphoramidite and convenient labeling of DNA oligonucleotide. Organic Letters, 2011, 13(8): 2000–2003 https://doi.org/10.1021/ol200397c
7	Sha R, Birktoft J J, Nguyen N, Chandrasekaran A R, Zheng J, Zhao X, Mao C, Seeman N C. Self-assembled DNA crystals: The impact on resolution of 5′-phosphates and the DNA source. Nano Letters, 2013, 13(2): 793–797 https://doi.org/10.1021/nl304550c
8	Han D, Jiang S, Samanta A, Liu Y, Yan H. Unidirectional scaffold–strand arrangement in DNA origami. Angewandte Chemie International Edition, 2013, 52(34): 9031–9034 https://doi.org/10.1002/anie.201302177
9	Frank-Kamenetskii M D, Mirkin S M. Triplex DNA structures. Annual Review of Biochemistry, 1995, 64(1): 65–95 https://doi.org/10.1146/annurev.bi.64.070195.000433
10	Lim K W, Phan A T. Structural basis of DNA quadruplex-duplex junction formation. Angewandte Chemie, 2013, 125(33): 8728–8731 https://doi.org/10.1002/ange.201302995
11	Ho P S, Eichman B F. The crystal structures of DNA Holliday junctions. Current Opinion in Structural Biology, 2001, 11(3): 302–308 https://doi.org/10.1016/S0959-440X(00)00219-0
12	Egli M. Nucleic acid crystallography: Current progress. Current Opinion in Chemical Biology, 2004, 8(6): 580–591 https://doi.org/10.1016/j.cbpa.2004.09.004
13	Lin L, Sheng J, Huang Z. Nucleic acid X-ray crystallography via direct selenium derivatization. Chemical Society Reviews, 2011, 40(9): 4591–4602 https://doi.org/10.1039/c1cs15020k
14	Zheng J, Birktoft J J, Chen Y, Wang T, Sha R, Constantinou P E, Ginell S L, Mao C, Seeman N C. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature, 2009, 461(7260): 74–77 https://doi.org/10.1038/nature08274
15	Egli M, Saenger W. In Principles of Nucleic Acid Structure. New York: Springer, 2013, 29–50
16	Berzelius J, Lettre de M, Berzelius à M. Berthollet sur deux métaux nouveaux. Letter from Mr.Berzelius to Mr. Berthollet on two new metals. Annales de chimie et de physique, series, 1818, 2: 199–206
17	Stadtman T C. Selenium biochemistry. Annual Review of Biochemistry, 1990, 59(1): 111–127 https://doi.org/10.1146/annurev.bi.59.070190.000551
18	Stadtman T C. Selenium biochemistry: Mammalian selenoenzymes. Annals of the New York Academy of Sciences, 2000, 899(1): 399–402 https://doi.org/10.1111/j.1749-6632.2000.tb06203.x
19	Zinoni F, Birkmann A, Stadtman T C, Böck A. Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 1986, 83(13): 4650–4654 https://doi.org/10.1073/pnas.83.13.4650
20	Böck A, Forchhammer K, Heider J, Leinfelder W, Sawers G, Veprek B, Zinoni F. Selenocysteine: The 21st amino acid. Molecular Microbiology, 1991, 5(3): 515–520 https://doi.org/10.1111/j.1365-2958.1991.tb00722.x
21	Hoffman J L, McConnell K P. The presence of 4-selenouridine in Escherichia coli tRNA. Biochimica et Biophysica Acta (BBA)-. Nucleic Acids and Protein Synthesis, 1974, 366(1): 109–113
22	Veres Z, Tsai L, Scholz T D, Politino M, Balaban R S, Stadtman T C. Synthesis of 5-methylaminomethyl-2-selenouridine in tRNAs: 31P NMR studies show the labile selenium donor synthesized by the selD gene product contains selenium bonded to phosphorus. Proceedings of the National Academy of Sciences of the United States of America, 1992, 89(7): 2975–2979 https://doi.org/10.1073/pnas.89.7.2975
23	Hendrickson W A, Pähler A, Smith J L, Satow Y, Merritt E A, Phizackerley R P. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. Proceedings of the National Academy of Sciences of the United States of America, 1989, 86(7): 2190–2194 https://doi.org/10.1073/pnas.86.7.2190
24	Hendrickson W A, Smith J L, Phizackerley R P, Merritt E A. Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. Proteins, 1988, 4(2): 77–88 https://doi.org/10.1002/prot.340040202
25	Hendrickson W A, Horton J R, Murthy H K, Pahler A, Smith J L. Multiwavelength anomalous diffraction as a direct phasing vehicle in macromolecular crystallography. In Synchrotron Radiation in Structural Biology. New York: Springer, 1989, 317–324
26	Hendrickson W A, Horton J R, LeMaster D M. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): A vehicle for direct determination of three-dimensional structure. EMBO Journal, 1990, 9(5): 1665–1672
27	Deacon A, Ealick S. Selenium-based MAD phasing: Setting the sites on larger structures. Structure (London, England), 1999, 7(7): 161–166 https://doi.org/10.1016/S0969-2126(99)80096-3
28	Carrasco N, Ginsburg D, Du Q, Huang Z. Synthesis of selenium-derivatized nucleosides and oligonucleotides for X-ray crystallography. Nucleosides, Nucleotides & Nucleic Acids, 2001, 20(9): 1723–1734 https://doi.org/10.1081/NCN-100105907
29	Sheng J, Huang Z. Selenium derivatization of nucleic acids for X-ray crystal–structure and function studies. Chemistry & Biodiversity, 2010, 7(4): 753–785 https://doi.org/10.1002/cbdv.200900200
30	Zhang W, Sheng J, Huang Z. Structures and functions of nucleic acids modified with S, Se, and Te and complexed with small molecules. Medicinal Chemistry of Nucleic Acids, 2011: 101–141
31	Jiang J, Sheng J, Carrasco N, Huang Z. Selenium derivatization of nucleic acids for crystallography. Nucleic Acids Research, 2007, 35(2): 477–485 https://doi.org/10.1093/nar/gkl1070
32	Teplova M, Wilds C J, Wawrzak Z, Tereshko V, Du Q, Carrasco N, Huang Z, Egli M. Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: Proof of principle. Biochimie, 2002, 84(9): 849–858 https://doi.org/10.1016/S0300-9084(02)01440-2
33	Ferré-D’Amaré A R, Zhou K, Doudna J A. A general module for RNA crystallization. Journal of Molecular Biology, 1998, 279(3): 621–631 https://doi.org/10.1006/jmbi.1998.1789
34	Ke A, Doudna J A. Crystallization of RNA and RNA-protein complexes. Methods (San Diego, Calif.), 2004, 34(3): 408–414 https://doi.org/10.1016/j.ymeth.2004.03.027
35	Salon J, Chen G, Portilla Y, Germann M W, Huang Z. Synthesis of a 2'-Se-uridine phosphoramidite and its incorporation into oligonucleotides for structural study. Organic Letters, 2005, 7(25): 5645–5648 https://doi.org/10.1021/ol052270y
36	Du Q, Carrasco N, Teplova M, Wilds C J, Egli M, Huang Z. Internal derivatization of oligonucleotides with selenium for X-ray crystallography using MAD. Journal of the American Chemical Society, 2002, 124(1): 24–25 https://doi.org/10.1021/ja0171097
37	Carrasco N, Buzin Y, Tyson E, Halpert E, Huang Z. Selenium derivatization and crystallization of DNA and RNA oligonucleotides for X-ray crystallography using multiple anomalous dispersion. Nucleic Acids Research, 2004, 32(5): 1638–1646 https://doi.org/10.1093/nar/gkh325
38	Sheng J, Salon J, Gan J, Huang Z. Synthesis and crystal structure study of 2′-Se-adenosine-derivatized DNA. Science China. Chemistry, 2010, 53(1): 78–85 https://doi.org/10.1007/s11426-010-0012-4
39	Salon J, Sheng J, Gan J, Huang Z. Synthesis and crystal structure of 2′-Se-modified guanosine containing DNA. Journal of Organic Chemistry, 2010, 75(3): 637–641 https://doi.org/10.1021/jo902190c
40	Sheng J, Jiang J, Salon J, Huang Z. Synthesis of a 2'-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study. Organic Letters, 2007, 9(5): 749–752 https://doi.org/10.1021/ol062937w
41	Moroder H, Kreutz C, Lang K, Serganov A, Micura R. Synthesis, oxidation behavior, crystallization and structure of 2'-methylseleno guanosine containing RNAs. Journal of the American Chemical Society, 2006, 128(30): 9909–9918 https://doi.org/10.1021/ja0621400
42	Höbartner C, Rieder R, Kreutz C, Puffer B, Lang K, Polonskaia A, Serganov A, Micura R. Syntheses of RNAs with up to 100 nucleotides containing site-specific 2'-methylseleno labels for use in X-ray crystallography. Journal of the American Chemical Society, 2005, 127(34): 12035–12045 https://doi.org/10.1021/ja051694k
43	Olieric V, Rieder U, Lang K, Serganov A, Schulze-Briese C, Micura R, Dumas P, Ennifar E. A fast selenium derivatization strategy for crystallization and phasing of RNA structures. RNA (New York, N.Y.), 2009, 15(4): 707–715 https://doi.org/10.1261/rna.1499309
44	Sheng J, Gan J, Soars A S, Salon J, Huang Z. Structural insights of non-canonical U·U pair and Hoogsteen interaction probed with Se atom. Nucleic Acids Research, 2013, 41(22): 10476–10487 https://doi.org/10.1093/nar/gkt799
45	Salon J, Gan J, Abdur R, Liu H, Huang Z. Synthesis of 6-Se-guanosine RNAs for structural study. Organic Letters, 2013, 15(15): 3934–3937 https://doi.org/10.1021/ol401698n
46	Abdur R, Gerlits O O, Gan J, Jiang J, Salon J, Kovalevsky A Y, Chumanevich A A, Weber I T, Huang Z. Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides. Acta Crystallographica. Section D, Biological Crystallography, 2014, 70(2): 354–361 https://doi.org/10.1107/S1399004713027922
47	Hassan A E, Sheng J, Zhang W, Huang Z. High fidelity of base pairing by 2-selenothymidine in DNA. Journal of the American Chemical Society, 2010, 132(7): 2120–2121 https://doi.org/10.1021/ja909330m
48	Zhang L, Yang Z, Sefah K, Bradley K M, Hoshika S, Kim M J, Kim H J, Zhu G, Jimenez E, Cansiz S, Teng I T, Champanhac C, McLendon C, Liu C, Zhang W, Gerloff D L, Huang Z, Tan W, Benner S A. Evolution of functional six-nucleotide DNA. Journal of the American Chemical Society, 2015, 137(21): 6734–6737 https://doi.org/10.1021/jacs.5b02251

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