Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom
Wen Zhang, Jack W. Szostak, Zhen Huang
Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom
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.
selenium / DNA / RNA / nucleic acid / crystallization
[1] |
Eddy S R. Non-coding RNA genes and the modern RNA world. Nature Reviews. Genetics, 2001, 2(12): 919–929
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[3] |
Watson J D, Crick F H. Molecular structure of nucleic acids. Nature, 1953, 171(4356): 737–738
CrossRef
Google scholar
|
[4] |
Doherty E A, Doudna J A. Ribozyme structures and mechanisms. Annual Review of Biophysics and Biomolecular Structure, 2001, 30(1): 457–475
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[9] |
Frank-Kamenetskii M D, Mirkin S M. Triplex DNA structures. Annual Review of Biochemistry, 1995, 64(1): 65–95
CrossRef
Google scholar
|
[10] |
Lim K W, Phan A T. Structural basis of DNA quadruplex-duplex junction formation. Angewandte Chemie, 2013, 125(33): 8728–8731
CrossRef
Google scholar
|
[11] |
Ho P S, Eichman B F. The crystal structures of DNA Holliday junctions. Current Opinion in Structural Biology, 2001, 11(3): 302–308
CrossRef
Google scholar
|
[12] |
Egli M. Nucleic acid crystallography: Current progress. Current Opinion in Chemical Biology, 2004, 8(6): 580–591
CrossRef
Google scholar
|
[13] |
Lin L, Sheng J, Huang Z. Nucleic acid X-ray crystallography via direct selenium derivatization. Chemical Society Reviews, 2011, 40(9): 4591–4602
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[18] |
Stadtman T C. Selenium biochemistry: Mammalian selenoenzymes. Annals of the New York Academy of Sciences, 2000, 899(1): 399–402
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[34] |
Ke A, Doudna J A. Crystallization of RNA and RNA-protein complexes. Methods (San Diego, Calif.), 2004, 34(3): 408–414
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
[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
CrossRef
Google scholar
|
/
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