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Frontiers of Chemical Science and Engineering

ISSN 2095-0179

ISSN 2095-0187(Online)

CN 11-5981/TQ

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Front. Chem. Sci. Eng.    2016, Vol. 10 Issue (2) : 196-202    https://doi.org/10.1007/s11705-016-1565-3
REVIEW ARTICLE
Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom
Wen Zhang1,2,3,Jack W. Szostak2,Zhen Huang1,3,*()
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.
Keywords selenium      DNA      RNA      nucleic acid      crystallization     
Corresponding Author(s): Zhen Huang   
Online First Date: 08 April 2016    Issue Date: 19 May 2016
 Cite this article:   
Wen Zhang,Jack W. Szostak,Zhen Huang. Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom[J]. Front. Chem. Sci. Eng., 2016, 10(2): 196-202.
 URL:  
https://academic.hep.com.cn/fcse/EN/10.1007/s11705-016-1565-3
https://academic.hep.com.cn/fcse/EN/Y2016/V10/I2/196
Fig.1  Selenium atom specific modifications in nucleic acids
Chemical environment Physical factors Sample properties
Solution pHMetal ionBuffer typePrecipitantDetergent TemperatureTimeGravityViscosityPressureNucleationCrystallization method Nucleic acid homogeneityNucleic acid purityNucleic acid aggregationCross-links
Tab.1  Parameters affecting nucleic acid crystallization process
Fig.2  Comparison of native and Se-modified DNA crystals (GTGTACAC) under the same magnification. (a) Native DNA (0.1 mm×0.1 mm×0.1 mm grown over 2 months), (b) Se-DNA (0.4 mm×0.4 mm×0.4 mm grown over 2 weeks). The native and Se-functionalized DNAs were grown in the best known conditions (40 mmol/L sodium cacodylate, 12 mmol/L sperminetetrahydrochloride, 80 mmol/L potassium chloride, 20 mmol/L magnesium chloride, pH 7.0) for each DNA
Se-modifications Sequences Facilitations and studys PDB code
2′-SeMe-dU (5′-GdU2′-SeGTACAC-3′)2(5′-GdU2′-SeGT5-BrACAC-3′)2 Facilitate A-form DNA crystallization 2DLJ, 2GPX, 1Z7I
(5′-GdU2′-SeGT2-SeACAC-3′)2 Facilitate A-form DNA crystallization to study 2-Se-T function in improving base-pair fidelity 3HGD
(5′-GdU2′-SeGTAC5-SeAC-3′)2 Facilitate A-form DNA crystallization to study CG base-pair structure 3IJN
(5′-GdU2′-SeGT4-SeACAC-3′)2 Facilitate A-form DNA crystallization to study TA base-pair structure 2NSK
(5′-GdU2′-SeGT5-TeACAC-3′)2(5′-GdU2′-SeGT5-SeACAC-3′)2(5′-GdU2′-SeGT5-SACAC-3′)2(5′-GdU2′-SeGT5-OACAC-3′)2 Facilitate A-form DNA crystallization to study the importance of the DNA base modification 3KQ8, 3K18, 3IKI, 3LTR, 3LTU, 3IJK, 3HG8, 3FA1, 3BM0,
2′-SeMe-T (5′-GT2′-SeGTACAC-3′)2 Facilitate A-form DNA crystallization 2HC7
(5′-GT2′-SeGTACAC-3′)2 crosslinked with platinums Facilitate A-form DNA crystallization to study DNA crosslinked with cisplatin 4I1G, 4H5A, 4FP6
2′-SeMe-G (5′-GTG2′-SeTACAC-3′)2 Facilitate A-form DNA crystallization 3IFI
(5′-CG2′-SeCGAAUUAGCG-3′)2 (5′-GCAG2′-SeAGUUAAAUCUGC-3′)2 Facilitate RNA crystallization 2H1M
2′-SeMe-A (5′-GTACGCGTA2′-SeC-3′)2 Facilitate A-form DNA crystallization 3IFF
2-Se-T (5′-GTGT2-SeACAC-3′)2 Facilitate A-form DNA crystallization 4F4N
2′-SeMe-ara-G (5′-CGCGAATTCG2′-SeCG-3′)2 Facilitate B-form DNA crystallization 4KW0
5-Se-T 5′-GT5-SeGTZACAC-3′/5′-GT5-SeGTPACAC-3′ Facilitate A-form DNA crystallization to study novel ZP base-pair structure 4RHD
Tab.2  Nucleic acid crystallization facilitated by the Se-modifications
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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