Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization

Nucleic Acids Research

Volumn 39, Issue 9, 2011, Pages 3962-3971

  Sheng, Jia ^a   Hassan, Abdalla E A ^a,b   Zhang, Wen ^a   Zhou, Jianfeng ^c   Xu, Bingqian ^c   Soares, Alexei S ^d   Huang, Zhen ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

^b ZAGAZIG UNIVERSITY   (Egypt)

^c UNIVERSITY OF GEORGIA   (United States)

^d BROOKHAVEN NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 PHENYLTELLURIDE THYMIDINE PHOSPHORAMIDITE; ADENOSINE; DOUBLE STRANDED DNA; OLIGODEOXYRIBONUCLEOTIDE; PHOSPHORAMIDOUS ACID DERIVATIVE; TELLURIUM; THYMIDINE; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA BASE COMPOSITION; DNA DENATURATION; DNA DETERMINATION; MOLECULAR IMAGING; MOLECULAR INTERACTION; NUCLEIC ACID ANALYSIS; NUCLEOTIDE METABOLISM; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SCANNING TUNNELING MICROSCOPY; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; THERMOSTABILITY;

CRYSTALLOGRAPHY, X-RAY; DNA; MICROSCOPY, SCANNING TUNNELING; MODELS, MOLECULAR; NUCLEIC ACID DENATURATION; OLIGODEOXYRIBONUCLEOTIDES; ORGANOPHOSPHORUS COMPOUNDS; TELLURIUM; THYMIDINE;

EID: 79956005796     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1288     Document Type: Article

References (49)

1. Zheng, J., Birktoft, J.J., Chen, Y., Wang, T., Sha, R., Constantinou, P.E., Ginell, S.L., Mao, C. and Seeman, N.C. (2009) From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature, 461, 74-77.
2. Xue, X., Wang, F. and Liu, X. (2008) One-step, room temperature, colorimetric detection of mercury (Hg2+) using DNA/ nanoparticle conjugates. J. Am. Chem. Soc., 130, 3244-3245. (Pubitemid 351456001)
3. Rothemund, P.W. (2006) Folding DNA to create nanoscale shapes and patterns. Nature, 440, 297-302.
4. Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M.M., Sander, B., Stark, H. and Oliveira, C.L. (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 459, 73-76.
5. Singer, A., Wanunu, M., Morrison, W., Kuhn, H., Frank- Kamenetskii, M. and Meller, A. (2010) Nanopore based sequence specific detection of duplex DNA for genomic profiling. Nano Lett., 10, 738-742.
6. Tiemann, K. and Rossi, J.J. (2009) RNAi-based therapeutics-current status, challenges and prospects. EMBO Mol. Med., 1, 142-151.
7. Huang, Y.C. and Sen, D. (2010) A contractile electronic switch made of DNA. J. Am. Chem. Soc., 132, 2663-2671.
8. Kratochvilova, I., Kral, K., Buncek, M., Viskova, A., Nespurek, S., Kochalska, A., Todorciuc, T., Weiter, M. and Schneider, B. (2008) Conductivity of natural and modified DNA measured by scanning tunneling microscopy. The effect of sequence, charge and stacking. Biophys. Chem., 138, 3-10.
9. Ito, T. and Rokita, S.E. (2004) Criteria for efficient transport of excess electrons in DNA. Angew. Chem. Int. Ed. Engl., 43, 1839-1842. (Pubitemid 39257838)
10. Barnett, R.N., Cleveland, C.L., Joy, A., Landman, U. and Schuster, G.B. (2001) Charge migration in DNA: ion-gated transport. Science, 294, 567-571. (Pubitemid 32999548)
11. Porath, D., Bezryadin, A., de Vries, S. and Dekker, C. (2000) Direct measurement of electrical transport through DNA molecules. Nature, 403, 635-638. (Pubitemid 30103998)
12. Fink, H.W. and Schonenberger, C. (1999) Electrical conduction through DNA molecules. Nature, 398, 407-410. (Pubitemid 29180369)
13. Yang, Z., Chen, F., Chamberlin, S.G. and Benner, S.A. (2010) Expanded genetic alphabets in the polymerase chain reaction. Angew. Chem. Int. Ed. Engl., 49, 177-180.
14. Hassan, A.E., Sheng, J., Zhang, W. and Huang, Z. (2010) High fidelity of base pairing by 2-selenothymidine in DNA. J. Am. Chem. Soc., 132, 2120-2121.
15. Egli, M. and Pallan, P.S. (2010) Crystallographic studies of chemically modified nucleic acids: a backward glance. Chem. Biodivers., 7, 60-89.
16. Ljungman, M. (2009) Targeting the DNA damage response in cancer. Chem. Rev., 109, 2929-2950.
17. Delaney, J.C., Gao, J., Liu, H., Shrivastav, N., Essigmann, J.M. and Kool, E.T. (2009) Efficient replication bypass of size-expanded DNA base pairs in bacterial cells. Angew. Chem. Int. Ed. Engl., 48, 4524-4527.
18. Sismour, A.M. and Benner, S.A. (2005) The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system. Nucleic Acids Res., 33, 5640-5646. (Pubitemid 41548830)
19. Kim, T.W., Delaney, J.C., Essigmann, J.M. and Kool, E.T. (2005) Probing the active site tightness of DNA polymerase in subangstrom increments. Proc. Natl Acad. Sci. USA, 102, 15803-15808. (Pubitemid 41552823)
20. Coffer, J.L., Bigham, S.R., Li, X., Pinizzotto, R.F., Rho, Y.G., Pirtle, R.M. and Pirtle, I.L. (1996) Dictation of the shape of mesoscale semiconductor nanoparticle assemblies by plasmid DNA. Appl. Phys. Lett., 69, 3851-3853. (Pubitemid 126593070)
21. Braun, E., Eichen, Y., Sivan, U. and Ben-Yoseph, G. (1998) DNA-templated assembly and electrode attachment of a conducting silver wire. Nature, 391, 775-778. (Pubitemid 28099671)
22. Ma, Y., Zhang, J., Zhang, G. and He, H. (2004) Polyaniline nanowires on Si surfaces fabricated with DNA templates. J. Am. Chem. Soc., 126, 7097-7101. (Pubitemid 38855408)
23. Elias, B., Shao, F. and Barton, J.K. (2008) Charge migration along the DNA duplex: hole versus electron transport. J. Am. Chem. Soc., 130, 1152-1153. (Pubitemid 351170990)
24. Guo, X., Gorodetsky, A.A., Hone, J., Barton, J.K. and Nuckolls, C. (2008) Conductivity of a single DNA duplex bridging a carbon nanotube gap. Nat. Nanotechnol., 3, 163-167. (Pubitemid 351355135)
25. Sheng, J., Hassan, A.E. and Huang, Z. (2008) New telluride-mediated elimination for novel synthesis of 20,30- didehydro-20,30-dideoxynucleosides. J. Org. Chem., 73, 3725-3729. (Pubitemid 351671436)
26. Sheng, J., Hassan, A.E. and Huang, Z. (2009) Synthesis of the first tellurium-derivatized oligonucleotides for structural and functional studies. Chem. Eur. J., 15, 10210-10216.
27. Moroder, L. (2005) Isosteric replacement of sulfur with other chalcogens in peptides and proteins. J. Pept. Sci., 11, 187-214. (Pubitemid 40542352)
28. Sheng, J. and Huang, Z. (2008) Selenium derivatization of nucleic acids for phase and structure determination in nucleic acid X-ray crystallography. Int. J. Mol. Sci., 9, 258-271. (Pubitemid 351482114)
29. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Method. Enzym., 276, 307-326. (Pubitemid 27085611)
30. McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C. and Read, R.J. (2007) Phaser crystallographic software. J. Appl. Crystallogr., 40, 658-674. (Pubitemid 47080256)
31. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S. et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr., 54, 905-921.
32. Murshudov, G.N., Vagin, A.A. and Dodson, E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr., 53, 240-255. (Pubitemid 27235885)
33. Parkinson, G., Vojtechovsky, J., Clowney, L., Brunger, A.T. and Berman, H.M. (1996) New parameters for the refinement of nucleic acid-containing structures. Acta Crystallogr. D Biol. Crystallogr., 52, 57-64. (Pubitemid 126512683)
34. Brunger, A.T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-475.
35. Read, R.J. (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A, 42, 140-149.
36. Rose, F., Martin, P., Fujita, H. and Kawakatsu, H. (2006) Adsorption and combing of DNA on HOPG surfaces of bulk crystals and nanosheets: application to the bridging of DNA between HOPG/Si heterostructures. Nanotechnology, 17, 3325-3332. (Pubitemid 44149669)
37. Naganara, L.A., Thundat, T. and Lindsay, S.M. (1989) Preparation and characterization of STM tips for electrochemical studies. Rev. Sci. Instrum., 60, 3128-3130.
38. Schinazi, R.F., Arbiser, J., Lee, J.J., Kalman, T.I. and Prusoff, W.H. (1986) Synthesis and biological activity of 5-phenylselenenyl-substituted pyrimidine nucleosides. J. Med. Chem., 29, 1293-1295. (Pubitemid 16059066)
39. Bergstrom, D., Beal, P., Husain, A., Lind, R. and Jenson, J. (1989) Palladium-mediated coupling between organic disulfides and nucleic acid constituents. J. Am. Chem. Soc., 111, 374-375.
40. Hirota, K., Tomishi, T., Maki, Y. and Sajiki, H. (1998) Synthesis of 5-arylthiouridines via electrophilic substitution of 5-bromouridines with diaryl disulfides. Nucleosides, Nucleotides and Nucleic Acids, 17, 161-173. (Pubitemid 28141532)
41. Zeng, Y., Cao, H. and Wang, Y. (2006) Facile Photocyclization Chemistry of 5-Phenylthio-2'-deoxyuridine in Duplex DNA. Organic Lett., 8, 2527-2530. (Pubitemid 43980434)
42. Lee, C. and Kim, Y. (1991) Direct regioselective arylsulfenylation and arylselenenylation at 5-position of uracils mediated by silver reagents. Tetrahedron Lett., 32, 2401-2404.
43. Ahmadian, M., Zhang, P. and Bergstrom, D.E. (1998) A comparative study of the thermal stability of oligodeoxyribonucleotides containing 5-substituted 20-deoxyuridines. Nucleic Acids Res., 26, 3127-3135. (Pubitemid 28288909)
44. Hayakawa, H., Tanaka, H., Obi, K., Itoh, M. and Miyasaka, T. (1987) A simple and general entry to 5-substituted uridines based on regioselective lithiation controlled by a protecting group in the sugar moiety. Tetrahedron Lett., 28, 87-90.
45. Karino, N., Ueno, Y. and Matsuda, A. (2001) Synthesis and properties of oligonucleotides containing 5-formyl-20- deoxycytidine: in vitro DNA polymerase reactions on DNA templates containing 5-formyl-20-deoxycytidine. Nucleic Acids Res., 29, 2456-2463. (Pubitemid 32600299)
46. Jiang, J., Sheng, J., Carrasco, N. and Huang, Z. (2007) Selenium derivatization of nucleic acids for crystallography. Nucleic Acids Res., 35, 477-485. (Pubitemid 46237389)
47. Salon, J., Sheng, J., Gan, J. and Huang, Z. (2010) Synthesis and crystal structure of 20-se-modified guanosine containing DNA. J. Org. Chem., 75, 637-641.
48. Sheng, J., Salon, J., Gan, J. and Huang, Z. (2010) Synthesis and crystal structure study of 20-Se-adenosine-derivatized DNA. Sci. China: Chem., 53, 78-85.
49. Jain, S., Zon, G. and Sundaralingam, M. (1989) Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGT ACAC). Biochemistry, 28, 2360-2364. (Pubitemid 19094346)