Synthesis and structural characterization of piperazino-modified DNA that favours hybridization towards DNA over RNA

Nucleic Acids Research

Volumn 39, Issue 5, 2011, Pages 1953-1965

  Skov, Joan ^a   Bryld, Torsten ^a   Lindegaard, Dorthe ^a   Nielsen, Katrine E ^a   Højland, Torben ^a   Wengel, Jesper ^a   Petersen, Michael ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

4' C (N METHYLPIPERAZINO)METHYLTHYMIDINE; DNA; PYRENE; RNA; THYMIDINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DNA DENATURATION; DNA HYBRIDIZATION; DNA STRUCTURE; DNA SYNTHESIS; FLUORESCENCE SPECTROSCOPY; INTERCALATION COMPLEX; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN MODIFICATION; RNA HYBRIDIZATION; ULTRAVIOLET SPECTROSCOPY;

CIRCULAR DICHROISM; DNA; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; PIPERAZINES; PYRENES; RNA; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, ULTRAVIOLET; THYMIDINE;

EID: 79953132000     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1123     Document Type: Article

References (39)

1. Seeman N.C. (2003) At the crossroads of chemistry biology and materials: structural DNA nanotechnology. Chem. Biol. 10 1151-1159. (Pubitemid 38042720)
2. Feldkamp U. and Niemeyer C.M. (2006) Rational design of DNA nanoarchitectures. Angew. Chem. Int. Ed. 45 1856-1876. (Pubitemid 44105204)
3. Seeman N.C. (2007) An overview of structural DNA nanotechnology. Mol. Biotechnol. 37 246-257. (Pubitemid 350242563)
4. Aldaye F.A. Palmer A.L. and Sleiman H.F. (2008) Assembling materials with DNA as the guide. Science 321 1795-1799.
5. Wengel J. (2004) Nucleic acid nanotechnology - towards Angstrom-scale engineering. Org. Biomol. Chem. 2 277-280.
6. Sessler J.L. and Jayawickramarajah J. (2005) Functionalized base-pairs: versatile scaffolds for self-assembly. Chem. Comm. 1939-1949. (Pubitemid 40613069)
7. Egli M. and Pallan P.S. (2010) The many twists and turns of DNA: template telomere tool and target. Curr. Opin. Struct. Biol. 20 262-275.
8. Raunkjær M. Bryld T. and Wengel J. (2003) Nmethylpiperazinocarbonyl- 20 30-BcNA and 40-C-(Nmethylpiperazino) methyl-DNA: introduction of basic functionalities facing the major groove and the minor groove of a DNA:DNA duplex. Chem. Comm. 1604-1605. (Pubitemid 36782915)
9. Bryld T. Højland T. and Wengel J. (2004) DNA-selective hybridization and dual strand invasion of short double-stranded DNA using pyren-1-ylcarbonyl-functionalized 40-Cpiperazinomethyl- DNA. Chem. Comm. 1064-1065. (Pubitemid 38662082)
10. Varghese R. and Wagenknecht H.A. (2009) DNA as a supramolecular framework for the helical arrangements of chromophores: towards photoactive DNA-based nanomaterials. Chem. Comm. 2615-2624.
11. Malinovskii V.L. Wenger D. and Haner R. (2010) Nucleic acid-guided assembly of aromatic chromophores. Chem. Soc. Rev. 39 410-422.
12. Delaglio F. Grzesiek S. Vuister G.W. Zhu G. Pfeifer J. and Bax A. (1995) NMRPipe - a multidimensional spectral processing system based on Unix pipes. J. Biomol. NMR 6 277-293.
13. Goddard T.D. and Kneller D.G. SPARKY 3. University of California San Francisco.
14. Glasoe P.K. and Long F.A. (1960) Use of glass electrodes to measure acidities in deuterium oxide. J. Phys. Chem. 64 188-190.
15. Song J.K. Laskowski M. Qasim M.A. and Markley J.L. (2003) NMR determination of pK(a) values for Asp Glu His and Lys mutants at each variable contiguous enzyme-inhibitor contact position of the turkey ovomucoid third domain. Biochemistry 42 2847-2856. (Pubitemid 36331528)
16. Bayly C.I. Cieplak P. Cornell W.D. and Kollman P.A. (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP dodel. J. Phys. Chem. 97 10269-10280.
17. Brunger A.T. (1996) X-PLOR version 3 851. Yale University Press New Haven CT.
18. Cornell W.D. Cieplak P. Bayly I. Gould I.R. Merz K.M. Ferguson D.M. Spellmeyer D.C. Fox T. Caldwell J.W. and Kollman P.A. (1995) A second generation force field for the simulation of proteins nucleic acids and organic molecules. J. Am. Chem. Soc. 117 5179-5197.
19. Pearlman D.A. Case D.A. Caldwell J.W. Ross W.S. Cheatham T.E. III DeBolt S. Ferguson D.M. Seibel G.L. and Kollman P.A. (1995) AMBER a package of computer programs for applying molecular mechanics normal mode analysis molecular dynamics and free energy calculations. Comp. Phys. Commun. 91 1-41.
20. Tsui V. and Case D.A. (2000) Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 56 275-291. (Pubitemid 34105875)
21. Thrane H. Fensholdt J. Regner M. and Wengel J. (1995) Novel linear and branched oligodeoxynucleotide analogs containing 40-C-(hydroxymethyl)thymidine. Tetrahedron 51 10389-10402.
22. Mokhir A.A. Tetzlaff C.N. Herzberger S. Mosbacher A. and Richert C. (2001) Monitored selection of DNA-hybrids forming duplexes with capped terminal C:G base pairs. J. Comb. Chem. 3 374-386. (Pubitemid 33614516)
23. Yamana K. Iwase R. Furutani S. Tsuchida H. Zako H. Yamaoka T. and Murakami A. (1999) 20-Pyrene modified oligonucleotide provides a highly sensitive fluorescent probe of RNA. Nucleic Acids Res. 27 2387-2392. (Pubitemid 29245659)
24. Wijmenga S.S. Kruithof M. and Hilbers C.W. (1997) Analysis of H-1 chemical shifts in DNA: assessment of the reliability of H-1 chemical shift calculations for use in structure refinement. J. Biomol. NMR 10 337-350. (Pubitemid 127505374)
25. Van Wijk J. Huckriede B.D. Ippel J.H. and Altona C. (1992) Furanose sugar conformations in DNA from NMR coupling constants. Methods Enzymol. 211 286-306.
26. Gorenstein D.G. (1994) Conformation and dynamics of DNA and protein-DNA complexes by P-31 NMR. Chem. Rev. 94 1315-1338. (Pubitemid 24987610)
27. Kanazaki M. Ueno Y. Shuto S. and Matsuda A. (2000) Highly nuclease-resistant phosphodiester-type oligodeoxynucleotides containing 40a-C-aminoalkylthymidines form thermally stable duplexes with DNA and RNA. A candidate for potent antisense molecules. J. Am. Chem. Soc. 122 2422-2432. (Pubitemid 30211951)
28. Smirnov S. Matray T.J. Kool E.T. and de los Santos C. (2002) Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites. Nucleic Acids Res. 30 5561-5569. (Pubitemid 36113933)
29. Nielsen C.B. Petersen M. Pedersen E.B. Hansen P.E. and Christensen U.B. (2004) NMR structure determination of a modified DNA oligonucleotide containing a new intercalating nucleic acid. Bioconjugate Chem. 15 260-269. (Pubitemid 38365185)
30. Pradhan P. Jernstrom B. Seidel A. Norden B. and Graslund A. (1998) Induced circular dichroism of benzo[a]pyrene-7 8-dihydrodiol-9 10-epoxide stereoisomers covalently bound to deoxyribooligonucleotides used to probe equilibrium distribution between groove binding and intercalative adduct conformations. Biochemistry 37 4664-4673. (Pubitemid 28217185)
31. Honcharenko D. Zhou C.Z. and Chattopadhyaya J. (2008) Modulation of pyrene fluorescence in DNA probes depends upon the nature of the conformationally restricted nucleotide. J. Org. Chem. 73 2829-2842. (Pubitemid 351482995)
32. Han X.G. and Gao X.L. (2001) Sequence specific recognition of ligand-DNA complexes studied by NMR. Curr. Med. Chem. 8 551-581.
33. Rodger A. and Nordén B. (1997) Circular Dichroism and Linear Dichroism. Oxford University Press Oxford.
34. Christensen U.B. and Pedersen E.B. (2002) Intercalating nucleic acids containing insertions of 1-O-(1-pyrenylmethyl)glycerol: stabilisation of dsDNA and discrimination of DNA over RNA. Nucleic Acids Res. 30 4918-4925. (Pubitemid 35414652)
35. Nakamura M. Fukunaga Y. Sasa K. Ohtoshi Y. Kanaori K. Hayashi H. Nakano H. and Yamana K. (2005) Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference. Nucleic Acids Res. 33 5887-5895. (Pubitemid 41742608)
36. Baruah H. and Bierbach U. (2003) Unusual intercalation of acridin-9-ylthiourea into the 50-GA/TC DNA base step from the minor groove: implications for the covalent DNA adduct profile of a novel platinum- intercalator conjugate. Nucleic Acids Res. 31 4138-4146. (Pubitemid 37442293)
37. Marx A. Erdmann P. Senn M. Korner S. Jungo T. Petretta M. Imwinkelried P. Dussy A. Kulicke K.J. Macko L. et al. (1996) Synthesis of 40-C-acylated thymidines. Helv. Chim. Acta 79 1980-1994.
38. Pfundheller H.M. Bryld T. Olsen C.E. and Wengel J. (2000) Oligonucleotides containing novel 40-C- or 30-C-(aminoalkyl)- branched thymidines. Helv. Chim. Acta 83 128-151. (Pubitemid 30077839)
39. Berman H.M. Neidle S. and Stodola R.K. (1978) Drug-nucleic acid interactions - conformational flexibility at intercalation site. Proc. Natl Acad. Sci. USA 75 828-832. (Pubitemid 8319467)