Pyrene intercalating nucleic acids with a carbon linker

Nucleosides, Nucleotides and Nucleic Acids

Volumn 30, Issue 3, 2011, Pages 210-226

  Østergaard, Michael E ^a   Wamberg, Michael C ^a   Pedersen, Erik B ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

INA; Intercalating nucleic acids; pyrene intercalators

Indexed keywords

1 O (1 PYRENYLMETHYL)GLYCEROL; BISPYRENE; CARBENE; CARBON; GLYCEROL; NUCLEIC ACID; OLIGONUCLEOTIDE; OXYGEN; PYRENE; PYRENE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL STRUCTURE; FLUORESCENCE ANALYSIS; INTERCALATION COMPLEX; MELTING POINT; SUBSTITUTION REACTION; SYNTHESIS; TEMPERATURE MEASUREMENT; THERMOSTABILITY;

INTERCALATING AGENTS; MOLECULAR STRUCTURE; NUCLEIC ACIDS; PYRENES; TRANSITION TEMPERATURE;

EID: 79956159709     PISSN: 15257770     EISSN: 15322335     Source Type: Journal    
DOI: 10.1080/15257770.2011.567202     Document Type: Article

References (26)

1. Filichev, V.V.; Pedersen, E.B. DNA-conjugated organic chromophores in DNA stacking interactions. In Wiley Encyclopedia of Chemical Biology, Ed. T. Begley, 2009.
2. Smirnov, S.; Matray, T.J.; Kool, E.T.; Santos, C. Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites. Nucleic Acids Res. 2002, 30, 5561-5569. (Pubitemid 36113933)
3. Winnik, F.M. Photophysics of preassociated pyrenes in aqueous polymer solutions and in other organized media. Chem. Rev. 1993, 93, 587-614.
4. Christensen, U.B.; Pedersen, E.B. Intercalating nucleic acids containing insertions of 1-O-(1- pyrenylmethyl)glycerol: Stabilisation of dsDNA and discrimination of DNA over RNA. Nucleic Acids Res. 2002, 30, 4918-4925. (Pubitemid 35414652)
5. Filichev, V.V.; Hilmy, K.M.H.; Christensen, U.B.; Pedersen, E.B. Intercalating nucleic acids: The inversion of the stereocenter in 1-O-(pyren-1-ylmethyl)glycerol from R to S. Thermal stability towards ssDNA, ssRNA and its own type of oligodeoxynucleotides. Tetrahedron Lett. 2004, 45, 4907-4910. (Pubitemid 38738846)
6. Chrisensen, U.B.; Wamberg, M.; El-Essawy, F.A.G.; Ismail, A.E.-H.; Nielsen, C.B.; Filichev, V.V.; Jessen, C.H.; Petersen, M.; Pedersen, E.B. Intercalating nucleic acids: The influence of linker length and intercalator type on their duplex stabilities. Nucleosides, Nucelotides Nucleic Acids 2004, 23, 207-225. (Pubitemid 38351974)
7. Okamoto, A.; Ichiba, T.; Saito, I. Pyrene-labeled oligodeoxynucleotide probe for detecting base insertion by excimer fluorescence emission. J. Am. Chem. Soc. 2004, 126, 8364-8365. (Pubitemid 38917944)
8. Yamana, K.; Iwai, T.; Ohtani, Y.; Sato, S.; Nakamura, M.; Nakano, H. Bis-pyrene-labeled oligonucleotides: Sequence specificity of excimer and monomer fluorescence changes upon hybridization with DNA. Bioconjugate Chem. 2002, 13, 1266-1273. (Pubitemid 35420019)
9. Yamana, K.; Fukunaga, Y.; Ohtani, Y.; Sato, S.; Nakamura, M.; Kim, W.J.; Akaike, T.; Maruyama, A. DNA mismatch detection using a pyrene-excimer-forming probe. Chem. Commun. 2005, 2509-2511. (Pubitemid 40769166)
10. Hainke, S.; Arndt, S.; Seitz, O. Concise synthesis of aryl-C-nucleosides by Friedel-Crafts alkylation. Org. Biomol. Chem. 2005, 3, 4233-4238. (Pubitemid 41801595)
11. Gerard, B.; Sangji, S.; O'Leary, D.J.; Porco Jr., J.A. Enantioselective photocycloaddition mediated by chiral Brønsted acids: Asymmetric synthesis of the rocaglamides. J. Am. Chem. Soc. 2006, 128, 7754-7755. (Pubitemid 43945715)
12. Yamane, A. MagiProbe: A novel fluorescence quenching-based oligonucleotide probe carrying a fluorophore and an intercalator. Nucleic Acids Res. 2002, 30, e97/1-e97/8.
13. Dioubankova, N.N.; Malakhov, A.D.; Stetsenko, D.A.; Korshun, V.A. Detection of point mutations using pyrene-labeled DNA probes. Russ. Chem. Bull. 2004, 53, 463-470. (Pubitemid 38881768)
14. Christensen, U.B.; Pedersen, E.B. Intercalating nucleic acids with pyrene nucleotide analogues as next-nearest neighbors for excimer fluorescence detection of single-pointmutations under nonstringent hybridization conditions. Helv. Chim. Acta 2003, 86, 2090-2097. (Pubitemid 36899517)
15. Taniguchi, M.; Koga, K.; Yamada, S. Stereochemical studies-XXX: Stereoselective synthesis of Dribose from L-glutamic acid. Tetrahedron 1974, 30, 3547-3552.
16. Lock, G. Ber., Über abkömmlinge des pyrens. 1937, 70B, 926-930.
17. Mujeeb, A.; Kerwin, S.M.; Kenyon, G.L.; James, T.L. Solution structure of a conserved DNA sequence from the HIV-1 genome: restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra. Biochemistry 1993, 32, 13419-13431. (Pubitemid 24020216)
18. Riddell, F.G.; Robinson, M.J.T. Conformational effects in compounds with six-membered rings-VI: Conformational equilibria in 5-alkyl-1, 3-dioxane. Tetrahedron 1967, 23, 3417-3425.
19. Nielsen, C.B.; Petersen, M.; Pedersen, E.B.; Hansen, P.E.; Christensen, U.B. NMR structure determination of a modified DNA oligonucleotide containing a new intercalating nucleic acid. Bioconjugate Chem. 2004, 15, 260-269. (Pubitemid 38365185)
20. Yamana, K.; Iwase, R.; Furutani, S.; Tsuchida, H.; Zako, H.; Yamaoka, T.; Murakami, A. 2'-Pyrene modified oligonucleotide provides a highly sensitive fluorescent probe of RNA. Nucleic Acids Res. 1999, 27, 2387-2392. (Pubitemid 29245659)
21. See http://www.schrodinger.com.
22. Weiner, S.J.; Kollman, P.A.; Case, D.A.; Singh, U.C.; Ghio, C.; Alagona, G.; Profeta Jr., S.; Weiner, P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 1984, 106, 765-784. (Pubitemid 14548426)
23. Weiner, S.J.; Kollman, P.A.; Nguyen, D.T.; Case, D.A. An all atom force field for simulations of proteins and nucleic acid. J. Comp. Chem. 1986, 7, 230-252.
24. Still, W.C.; Tempczyk, A.; Hawley, R.C.; Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990, 112, 6127-6129.
25. van Gunsteren, W.F.; Berendsen, H.J.C. A leap-frog algorithm for stochastic dynamics. Mol. Simul. 1988, 1, 173-185.
26. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H.J.C. Numerical integration of the cartesian equation of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1997, 23, 327-341.