Top

Published in:

2013 | OriginalPaper | Chapter

3. Selenium Atom-Specific Mutagenesis (SAM) for Crystallography, DNA Nanostructure Design, and Other Applications

Authors : Sibo Jiang, Huiyan Sun, Zhen Huang

Published in: DNA Nanotechnology

Publisher: Springer Berlin Heidelberg

Activate our intelligent search to find suitable subject content or patents.

search-config

AI-assisted search

Off

Abstract

Since oxygen and selenium are in the same elemental family, the replacement of oxygen in nucleic acids with selenium does not significantly change the local as well as overall structures, which preserves the nucleic acid structures in a predictable manner. Furthermore, the valuable differences in chemical and electronic properties enable various functions and applications, including crystallization, phase determination, and high-resolution structure determination in X-ray crystallography, base-pair high fidelity, nanotechnology, and molecular imaging. This chapter briefly introduces the selenium-modified nucleic acids (SeNA), the selenium atom-specific mutagenesis (SAM), and their potentials in DNA nanotechnology.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

inform now

previous chapter Functional Nucleic Acids for DNA Nanotechnology

next chapter Liposomes for DNA Nanotechnology: Preparation, Properties, and Applications

Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737–738CrossRef

Beaucage S, Caruthers M (1981) Deoxynucleoside phosphoramidites—a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett 22:1859–1862CrossRef

Matteucci MD, Caruthers MH (1981) Synthesis of deoxyoligonucleotides on a polymer support. J Am Chem Soc 103:3185–3191CrossRef

Uhlmann E, Peyman A (1990) Antisense oligonucleotides: a new therapeutic principle. Chem Rev 90:543–584CrossRef

Milligan JF, Matteucci MD, Martin JC (1993) Current concepts in antisense drug design. J Med Chem 36:1923–1937CrossRef

Freier SM, Altmann KH (1997) The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA: RNA duplexes. Nucleic Acids Res 25:4429–4443CrossRef

Leumann CJ (2002) DNA analogues: from supramolecular principles to biological properties. Bioorg Med Chem 10:841–854CrossRef

Prakash TP, Bhat B (2007) 2′-modified oligonucleotides for antisense therapeutics. Curr Top Med Chem 7:641–649CrossRef

Weisbrod SH, Marx A (2008) Novel strategies for the site-specific covalent labelling of nucleic acids. Chem Commun (Camb) 44:5675–5685

10.

McManus MT, Sharp PA (2002) Gene silencing in mammals by small interfering RNAs. Nat Rev Genet 3:737–747CrossRef

11.

Dorsett Y, Tuschl T (2004) siRNAs: applications in functional genomics and potential as therapeutics. Nat Rev Drug Discov 3:318–329CrossRef

12.

Manoharan M (2004) RNA interference and chemically modified small interfering RNAs. Curr Opin Chem Biol 8:570–579CrossRef

13.

Watts JK, Deleavey GF, Damha MJ (2008) Chemically modified siRNA: tools and applications. Drug Discov Today 13:842–855CrossRef

14.

Gaynor JW, Campbell BJ, Cosstick R (2010) RNA interference: a chemist’s perspective. Chem Soc Rev 39:4169–4184CrossRef

15.

Sheng J, Huang Z (2010) Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies. Chem Biodivers 7:753–785CrossRef

16.

Lin L, Sheng J, Huang Z (2011) Nucleic acid X-ray crystallography via direct selenium derivatization. Chem Soc Rev 40:4591–4602CrossRef

17.

Sun H, Sheng J, Hassan AEA, Jiang S, Gan J, Huang Z (2012) Novel RNA base pair with higher specificity using single selenium atom. Nucleic Acids Res 40:5171–5179CrossRef

18.

Hassan AEA, Sheng J, Zhang W, Huang Z (2010) High fidelity of base pairing by 2-selenothymidine in DNA. J Am Chem Soc 132:2120–2121CrossRef

19.

Pallan PS, Prakash TP, Li F, Eoff RL, Manoharan M, Egli M (2009) A conformational transition in the structure of a 2′-thiomethyl-modified DNA visualized at high resolution. Chem Commun (Camb) 15:2017–2019

20.

Moroder H, Kreutz C, Lang K, Serganov A, Micura R (2006) Synthesis, oxidation behavior, crystallization and structure of 2′-methylseleno guanosine containing RNAs. J Am Chem Soc 128:9909–9918CrossRef

21.

Sheng J, Hassan AEA, Huang Z (2009) Synthesis of the first tellurium-derivatized oligonucleotides for structural and functional studies. Chem Eur J 15:10210–10216CrossRef

22.

Sheng J, Hassan AEA, Zhang W, Zhou J, Xu B, Soares AS, Huang Z (2011) Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization. Nucleic Acids Res 39:3962–3971CrossRef

23.

Jiang S, Sheng J, Huang Z (2011) Synthesis of the tellurium-derivatized phosphoramidites and their incorporation into DNA oligonucleotides. Curr Protoc Nucleic Acid Chem Chapter 1, Unit1.25.

24.

Carrasco N, Ginsburg D, Du Q, Huang Z (2001) Synthesis of selenium-derivatized nucleosides and oligonucleotides for X-ray crystallography. Nucleosides Nucleotides Nucleic Acids 20:1723–1734CrossRef

25.

Du Q, Carrasco N, Teplova M, Wilds CJ, Egli M, Huang Z (2002) Internal derivatization of oligonucleotides with selenium for X-ray crystallography using MAD. J Am Chem Soc 124:24–25CrossRef

26.

Teplova M, Wilds CJ, Wawrzak Z, Tereshko V, Du Q, Carrasco N, Huang Z, Egli M (2002) Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: proof of principle. Multiwavelength anomalous dispersion. Biochimie 84:849–858CrossRef

27.

Jiang J, Sheng J, Carrasco N, Huang Z (2007) Selenium derivatization of nucleic acids for crystallography. Nucleic Acids Res 35:477–485CrossRef

28.

Carrasco N, Buzin Y, Tyson E, Halpert E, Huang Z (2004) Selenium derivatization and crystallization of DNA and RNA oligonucleotides for X-ray crystallography using multiple anomalous dispersion. Nucleic Acids Res 32:1638–1646CrossRef

29.

Buzin Y, Carrasco N, Huang Z (2004) Synthesis of selenium-derivatized cytidine and oligonucleotides for X-ray crystallography using MAD. Org Lett 6:1099–1102CrossRef

30.

Höbartner C, Micura R (2004) Chemical synthesis of selenium-modified oligoribonucleotides and their enzymatic ligation leading to an U6 SnRNA stem-loop segment. J Am Chem Soc 126:1141–1149CrossRef

31.

Höbartner C, Rieder R, Kreutz C, Puffer B, Lang K, Polonskaia A, Serganov A, Micura R (2005) Syntheses of RNAs with up to 100 nucleotides containing site-specific 2′-methylseleno labels for use in X-ray crystallography. J Am Chem Soc 127:12035–12045CrossRef

32.

Sheng J, Jiang J, Salon J, Huang Z (2007) Synthesis of a 2′-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study. Org Lett 9:749–752CrossRef

33.

Salon J, Sheng J, Gan J, Huang Z (2010) Synthesis and crystal structure of 2′-se-modified guanosine containing DNA. J Org Chem 75:637–641CrossRef

34.

Sheng J, Salon J, Gan J, Huang Z (2010) Synthesis and crystal structure study of 2′-Se-adenosine-derivatized DNA. Sci China Chem 53:78–85CrossRef

35.

Gott JM, Willis MC, Koch TH, Uhlenbeck OC (1991) A specific, UV-induced RNA-protein cross-link using 5-bromouridine-substituted RNA. Biochemistry 30:6290–6295CrossRef

36.

Ennifar E, Carpentier P, Ferrer J, Walter P, Dumas P (2002) X-ray-induced debromination of nucleic acids at the BrK absorption edge and implications for MAD phasing. Acta Crystallogr D Biol Crystallogr 58:1262–1268CrossRef

37.

Reist E, Gueffroy D, Goodman L (1964) Synthesis of 4-thio-D- and -L-ribofuranose and the corresponding adenine nucleosides. J Am Chem Soc 86:5658–5663CrossRef

38.

Haeberli P, Berger I, Pallan PS, Egli M (2005) Syntheses of 4′-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4′-thiocytosine. Nucleic Acids Res 33:3965–3975CrossRef

39.

Dande P, Prakash TP, Sioufi N, Gaus H, Jarres R, Berdeja A, Swayze EE, Griffey RH, Bhat B (2006) Improving RNA interference in mammalian cells by 4′-thio-modified small interfering RNA (siRNA): effect on siRNA activity and nuclease stability when used in combination with 2′-O-alkyl modifications. J Med Chem 49:1624–1634CrossRef

40.

Inoue N, Shionoya A, Minakawa N, Kawakami A, Ogawa N, Matsuda A (2007) Amplification of 4′-thioDNA in the presence of 4′-thio-dTTP and 4′-thio-dCTP, and 4′-thioDNA-directed transcription in vitro and in mammalian cells. J Am Chem Soc 129:15424–15425CrossRef

41.

Inagaki Y, Minakawa N, Matsuda A (2007) Synthesis of 4′-selenoribonucleosides. Nucleic Acids Symp Ser 51:139–140

42.

Naka T, Minakawa N, Abe H, Kaga D, Matsuda A (2000) The stereoselective synthesis of 4′-thioribonucleosides via the Pummerer reaction. J Am Chem Soc 122:7233–7243CrossRef

43.

Inagaki Y, Minakawa N, Matsuda A (2008) Synthesis and properties of oligonucleotides containing 4′-selenoribonucleosides. Nucleic Acids Symp Ser 52:329–330

44.

Jeong LS, Tosh DK, Kim HO, Wang T, Hou X, Yun HS, Kwon Y, Lee SK, Choi J, Zhao LX (2008) First synthesis of 4′-selenonucleosides showing unusual Southern conformation. Org Lett 10:209–212CrossRef

45.

Jayakanthan K, Johnston BD, Pinto BM (2008) Stereoselective synthesis of 4′-selenonucleosides using the Pummerer glycosylation reaction. Carbohydr Res 343:1790–1800CrossRef

46.

Watts JK, Johnston BD, Jayakanthan K, Wahba AS, Pinto BM, Damha MJ (2008) Synthesis and biophysical characterization of oligonucleotides containing a 4′-selenonucleotide. J Am Chem Soc 130:8578–8579CrossRef

47.

Alexander V, Choi WJ, Chun J, Kim HO, Jeon JH, Tosh DK, Lee HW, Chandra G, Choi J, Jeong LS (2010) A new DNA building block, 4′-selenothymidine: synthesis and modification to 4′-seleno-AZT as a potential anti-HIV agent. Org Lett 12:2242–2245CrossRef

48.

Mori K, Boiziau C, Cazenave C, Matsukura M, Subasinghe C, Cohen JS, Broder S, Toulmé JJ, Stein CA (1989) Phosphoroselenoate oligodeoxynucleotides: synthesis, physico-chemical characterization, anti-sense inhibitory properties and anti-HIV activity. Nucleic Acids Res 17:8207–8219CrossRef

49.

Wilds CJ, Pattanayek R, Pan C, Wawrzak Z, Egli M (2002) Selenium-assisted nucleic acid crystallography: use of phosphoroselenoates for MAD phasing of a DNA structure. J Am Chem Soc 124:14910–14916CrossRef

50.

Egli M, Pallan PS, Pattanayek R, Wilds CJ, Lubini P, Minasov G, Dobler M, Leumann CJ, Eschenmoser A (2006) Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J Am Chem Soc 128:10847–10856CrossRef

51.

Pallan PS, Egli M (2007) Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives for crystallographic phasing of nucleic acid structures. Nat Protoc 2:640–646CrossRef

52.

Baraniak J, Korczynski D, Kaczmarek R, Stec WJ (1999) Tetra-thymidine phosphorofluoridates via tetra-thymidine phosphoro-selenoates: synthesis and stability. Nucleosides Nucleotides 18:2147–2154CrossRef

53.

Stawinski J, Thelin M (1994) Nucleoside H-phosphonates. 14. Synthesis of nucleoside phosphoroselenoates and phosphorothioselenoates via stereospecific selenization of the corresponding H-phosphonate and H-phosphonothioate diesters with the aid of new selenium-transfer reagent, 3H-1,2-benzothiaselenol-3-one. J Org Chem 59:130–136CrossRef

54.

Bollmark M, Stawinski J (2001) A new selenium-transferring reagent-triphenylphosphine selenide. Chem Commun (Camb) 8:771–772

55.

Holloway GA, Pavot C, Scaringe SA, Lu Y, Rauchfuss TB (2002) An organometallic route to oligonucleotides containing phosphoroselenoate. Chembiochem 3:1061–1065CrossRef

56.

Tram K, Wang X, Yan H (2007) Facile synthesis of oligonucleotide phosphoroselenoates. Org Lett 9:5103–5106CrossRef

57.

Guga P, Maciaszek A, Stec WJ (2005) Oxathiaphospholane approach to the synthesis of oligodeoxyribonucleotides containing stereodefined internucleotide phosphoroselenoate function. Org Lett 7:3901–3904CrossRef

58.

Caton-Williams J, Huang Z (2008) Synthesis and DNA-polymerase incorporation of colored 4-selenothymidine triphosphate for polymerase recognition and DNA visualization. Angew Chem Int Ed Engl 47(1723–1725)

59.

Sintim HO, Kool ET (2006) Enhanced base pairing and replication efficiency of thiothymidines, expanded-size variants of thymidine. J Am Chem Soc 128:396–397CrossRef

60.

Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 26:148–153CrossRef

61.

Shohda K, Okamoto I, Wada T, Seio K, Sekine M (2000) Synthesis and properties of 2′-O-methyl-2-thiouridine and oligoribonucleotides containing 2′-O-methyl-2-thiouridine. Bioorg Med Chem Lett 10:1795–1798CrossRef

62.

Ueda T, Iida Y, Ikeda K, Mizuno Y (1966) Synthesis of 2,4-dithiouridine and 2-thiocytidine. Chem Pharm Bull 14:666–667

63.

Vormbrock R, Morawietz R, Gassen HG (1974) Codon-anticodon interaction studies with trinucleoside diphosphates containing 2-thiouridine, 4-thiouridine, 2,4-diethiouridine, or 2-thiocytidine. Biochim Biophys Acta 340:348–358CrossRef

64.

Connolly BA, Newman PC (1989) Synthesis and properties of oligonucleotides containing 4-thiothymidine, 5-methyl-2-pyrimidinone-1-beta-D(2′-deoxyriboside) and 2-thiothymidine. Nucleic Acids Res 17:4957–4974CrossRef

65.

Rajeev KG, Prakash TP, Manoharan M (2003) 2′-modified-2-thiothymidine oligonucleotides. Org Lett 5:3005–3008CrossRef

66.

Kumar RK, Davis DR (1997) Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability. Nucleic Acids Res 25:1272–1280CrossRef

67.

Houssier C, Degée P, Nicoghosian K, Grosjean H (1988) Effect of uridine dethiolation in the anticodon triplet of tRNA(Glu) on its association with tRNA(Phe). J Biomol Struct Dyn 5:1259–1266CrossRef

68.

Agris PF, Söll D, Seno T (1973) Biological function of 2-thiouridine in Escherichia coli glutamic acid transfer ribonucleic acid. Biochemistry 12:4331–4337CrossRef

69.

Ashraf SS, Sochacka E, Cain R, Guenther R, Malkiewicz A, Agris PF (1999) Single atom modification (O–>S) of tRNA confers ribosome binding. RNA 5:188–194CrossRef

70.

Diop-Frimpong B, Prakash TP, Rajeev KG, Manoharan M, Egli M (2005) Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2′-O-[2-(methoxy)ethyl]-2-thiothymidines. Nucleic Acids Res 33:5297–5307CrossRef

71.

Coleman R, Siedlecki J (1992) Synthesis of a 4-thio-2‘-deoxyuridine containing oligonucleotide. Development of the thiocarbonyl group as a linker element. J Am Chem Soc 114:9229–9230CrossRef

72.

Christopherson MS, Broom AD (1991) Synthesis of oligonucleotides containing 2‘-deoxy-6-thioguanosine at a predetermined site. Nucleic Acids Res 19:5719–5724CrossRef

73.

Rappaport HP (1988) The 6-thioguanine/5-methyl-2-pyrimidinone base pair. Nucleic Acids Res 16:7253–7267CrossRef

74.

Favre A, Saintomé C, Fourrey JL, Clivio P, Laugâa P (1998) Thionucleobases as intrinsic photoaffinity probes of nucleic acid structure and nucleic acid-protein interactions. J Photochem Photobiol B Biol 42:109–124CrossRef

75.

Held HA, Benner SA (2002) Challenging artificial genetic systems: thymidine analogs with 5-position sulfur functionality. Nucleic Acids Res 30:3857–3869CrossRef

76.

Salon J, Sheng J, Jiang J, Chen G, Caton-Williams J, Huang Z (2007) Oxygen replacement with selenium at the thymidine 4-position for the Se base pairing and crystal structure studies. J Am Chem Soc 129:4862–4863CrossRef

77.

Logan G, Igunbor C, Chen G-X, Davis H, Simon A, Salon J, Huang Z (2006) A simple strategy for incorporation, protection, and deprotection of selenium functionality. Synlett 2006:1554–1558CrossRef

78.

Sheng J, Huang Z (2008) Synthesis of a 4-selenothymidine phosphoramidite and incorporation into oligonucleotides. Curr Protoc Nucleic Acid Chem Chapter 1, Unit 1.19

79.

Sismour AM, Benner SA (2005) The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system. Nucleic Acids Res 33:5640–5646CrossRef

80.

Wise DS, Townsend LB (1972) Synthesis of the selenopyrimidine nucleosides 2-seleno- and 4-selenouridine. J Heterocycl Chem 9:1461–1462CrossRef

81.

Shiue C-Y, Chu S-H (1975) A facile synthesis of 1-beta-D-arabinofuranosyl-2-seleno- and -4-selenouracil and related compounds. J Org Chem 40:2971–2974CrossRef

82.

Christofferson A, Zhao L, Sun H, Huang Z, Huang N (2011) Theoretical studies of the base pair fidelity of selenium-modified DNA. J Phys Chem B 115:10041–10048CrossRef

83.

Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM (2006) MODOMICS: a database of RNA modification pathways. Nucleic Acids Res 34:D145–149CrossRef

84.

Ching WM, Alzner-DeWeerd B, Stadtman TC (1985) A selenium-containing nucleoside at the first position of the anticodon in seleno-tRNAGlu from Clostridium sticklandii. Proc Natl Acad Sci U S A 82:347–350CrossRef

85.

Wittwer AJ, Tsai L, Ching WM, Stadtman TC (1984) Identification and synthesis of a naturally occurring selenonucleoside in bacterial tRNAs: 5-[(methylamino)methyl]-2-selenouridine. Biochemistry 23:4650–4655CrossRef

86.

Salon J, Jiang J, Sheng J, Gerlits OO, Huang Z (2008) Derivatization of DNAs with selenium at 6-position of guanine for function and crystal structure studies. Nucleic Acids Res 36:7009–7018CrossRef

87.

Zhang W, Sheng J, Hassan AE, Huang Z (2012) Synthesis of 2′-deoxy-5-(methylselenyl)cytidine and Se-DNAs for structural and functional studies. Chem Asian J 7:476–479CrossRef

88.

Carrasco N, Caton-Williams J, Brandt G, Wang S, Huang Z (2005) Efficient enzymatic synthesis of phosphoroselenoate RNA by using adenosine 5′-(alpha-P-seleno)triphosphate. Angew Chem Int Ed Engl 45:94–97

89.

Brandt G, Carrasco N, Huang Z (2006) Efficient substrate cleavage catalyzed by hammerhead ribozymes derivatized with selenium for X-ray crystallography. Biochemistry 45:8972–8977

90.

Lin L, Caton-Williams J, Kaur M, Patino AM, Sheng J, Punetha J, Huang Z (2011) Facile synthesis of nucleoside 5′-(alpha-P-seleno)-triphosphates and phosphoroselenoate RNA transcription. RNA 17(10):1932–1938

Title: Selenium Atom-Specific Mutagenesis (SAM) for Crystallography, DNA Nanostructure Design, and Other Applications
Authors: Sibo Jiang
Huiyan Sun
Zhen Huang
Publisher: Springer Berlin Heidelberg
Book: DNA Nanotechnology
Print ISBN: 978-3-642-36076-3

Electronic ISBN: 978-3-642-36077-0

Copyright Year: 2013
DOI: https://doi.org/10.1007/978-3-642-36077-0_3

Springer Professional

Abstract

Please log in to get access to your license.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Premium Partners