A pyrenyl-PNA probe for DNA and RNA recognition: Fluorescence and UV absorption studies

Artificial DNA: PNA and XNA

Volumn 1, Issue 2, 2010, Pages 83-89

  Tedeschi, Tullia ^a   Tonelli, Alessandro ^a   Sforza, Stefano ^a   Corradini, Roberto ^a   Marchelli, Rosangela ^a  

^a UNIVERSITY OF PARMA   (Italy)

Author keywords

DNA; Fluorescence; Peptide nucleic acid; Pyrene; RNA

Indexed keywords

DNA; GUANINE; GUANINE QUADRUPLEX; NUCLEIC ACID BASE; OLIGOMER; PEPTIDE NUCLEIC ACID; PYRENE DERIVATIVE; RNA;

ARTICLE; COVALENT BOND; DNA BINDING; DNA SEQUENCE; ENTHALPY; FLUORESCENCE ANALYSIS; FLUORESCENCE SPECTROSCOPY; MELTING POINT; MOLECULAR PROBE; MOLECULAR RECOGNITION; NUCLEIC ACID STRUCTURE; NUCLEOTIDE SEQUENCE; PROTEIN INTERACTION; RNA BINDING; RNA SEQUENCE; THERMODYNAMICS; ULTRAVIOLET SPECTROSCOPY;

EID: 79952180749     PISSN: 1949095X     EISSN: 19490968     Source Type: Journal    
DOI: 10.4161/adna.1.2.13899     Document Type: Article

References (43)

1. Wagenknecht HA. Fluorescent DNA base modifications and substitutes: multiple fluorophore labeling and the DETEQ Concept. Ann NY Acad Sci 2008; 1130:122-30.
2. Martí AA, Jockusch S, Stevens N, Ju J, Turro NJ. Fluorescent hybridization probes for sensitive and selective DNA and RNA detection. Acc Chem Res 2007; 40:402-9.
3. Rist MJ, Marino JP. Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions. Curr Org Chem 2002; 6:775-93.
4. Wojczewski C, Stolze K, Engels JW. Fluorescent oligonucleotides- Versatile tools as probes and primers for DNA and RNA analysis. Synlett 1999; 10:1667-78.
5. Winnik FM. Photophysics of preassociated pyrenes in aqueous polymer solutions and in other organized media. Chem Rev 1993; 93:587-614.
6. Wanninger-Weiß C, Wagenknecht HA. Synthesis of 5-(2-Pyrenyl)-2'-deoxyuridine as a DNA modification for electron-transfer studies: the critical role of the position of the chromophore attachment. Eur J Org Chem 2008; 1:64-71.
7. Okamoto A, Kanatani K, Saito S. Pyrene-labeled basediscriminating fluorescent DNA probes for homogeneous SNP typing. J Am Chem Soc 2004; 126:4820-7.
8. Kaden P, Mayer E, Trifonov A, Fiebig T, Wagenknecht HA. Real-Time spectroscopic and chemical probing of reductive electron transfer in DNA. Angew Chem Int Ed 2005; 44:1636-9.
9. Raytchev M, Mayer E, Amann N, Wagenknecht HA, Fiebig T. Ultrafast proton-coupled electron-transfer dynamics in pyrene-modified pyrimidine nucleosides: model studies towards an understanding of reductive electron transport in DNA. Chem Phys Chem 2004; 5:706-12.
10. Wagner C, Rist M, Mayer-Enthart E, Wagenknecht HA. 1-Ethynylpyrene-modified guanine and cytosineas optical labels for DNA hybridization. Org Biomol Chem 2005; 3:2062-3.
11. Mayer-Enthart E, Wagenknecht HA. Structuresensitive and self-assembled helical pyrene array based on DNA architecture. Angew Chem Int Ed 2006; 45:3372-5.
12. Honcharenko D, Zhou C, Chattopadhyaya J. Modulation of pyrene fluorescence in DNA probes depends upon the nature for the conformationally restricted nucleotide. J Org Chem 2008; 73:2829-42.
13. Christensen UB, Pedersen EB. Intercalating nucleic acids containing insertions of 1-O-(1-pyrenylmethyl) glycerol: stabilisation of dsDNA and discrimination of DNA over RNA. Nucleic. Acids Res 2002; 30:4918-25.
14. Kumar TS, Madesen AS, Ostergaard ME, Sau SP, Wengel J, Hirlldika PJ. Functionalized 2' amino-α-LLNA: directed positioning of intercalators for DNA targeting. J Org Chem 2009; 74:1070-81.
15. Fujiimoto K, Shimizu H, Inouye M. Unambiguous detection of Target DNAs by excimer-mnomer switching molecular beacons. J Org Chem 2004; 69:3271-5.
16. Wilson JN, Kool ET. Fluorescent DNA base replacements: reporters and sensors for biological systems. Org Biomol Chem 2006; 4:4265-74.
17. Nielsen PE, Egholm M, Berg RH, Buchardt O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 1991; 254:1497-500.
18. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, et al. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 1993; 365:556-68.
19. Pellestor F, Paulasova P. The use of peptide nucleic acids (PNAs) as probes in genetic and cytogenetic assays. Curr Top Genet 2006; 2:57-64.
20. Lundin E, Good L, Stroemberg R, Graeslund A, Smith CIE. Biological activity and biotechnological aspects of peptide nucleic acid. Adv Genet 2006; 56:1-51.
21. Brandt O, Hoheisel JD. Peptide nucleic acids on microarrays and other biosensors. Trends Biotechnol 2004; 22:617-22.
22. Sahu N, Shilakari G, Nayak A, Kohli DV. Peptide nucleic acids: a novel approach. Curr Chem Biol 2008; 2:110-21.
23. Totsingan F, Rossi S, Corradini R, Tedeschi T, Sforza S, Juris A, et al. Label-free selective DNA detection with high mismatch recognition by PNA beacons and ion exchange HPLC. Org Biomol Chem 2008; 6:1232-7.
24. Socher E, Bethge L, Knoll A, Jungnick N, Herrmann A, Seitz O. Low-Noise Stemless PNA Beacons for Sensitive DNA and RNA Detection. Angew Chem Int Ed 2008; 47:9555-9.
25. Lejion M, Mousavi-Jazi M, Kubista M. Light Up probes in clinical diagnostics. Mol Aspects Med 2006; 27:160-75.
26. Köhler O, Seitz O. Thiazole orange as fluorescent universal base in peptide nucleic acids. Chem Comm 2003; 2938-9.
27. Köhler O, Jarikote DV, Seitz O. Forced intercalation probes (FIT Probes): thiazole orange as a fluorescent base in peptide nucleic acids for homogeneous singlenucleotide- polymorphism detection. Chembiochem 2005; 6:69-77.
28. Socher E, Jarikote DP, Knoll A, Roglin L, Burmesteir J, Seitz O. FIT probes: peptide nucleic acid probes with a fluorescent base surrogate enable real-time DNA quantification and single nucleotide polymorphism discovery. Anal Biochem 2008; 375:318-30.
29. Mackinnon KF, Qualley DF, Wosky SA. Polycyclic aromatic hydrocarbons as universal bases in peptide nucleic acid. Tettrahedron Lett 2007; 8074-7.
30. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 2006; 34:5402-15.
31. Nakken S, Rognes T, Hovig E. The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts. Nucleic Acids Res 2009; 37:5749-56.
32. Onyshchenko MI, Gaynutdinov TI, Englund EA, Appella DH, Neumann RD, Panyutin IG. Stabilization of G-quadruplex in the BCL2 promoter region in double- stranded DNA by invading short PNAs. Nucleic Acids Res 2009; 37:7570-80.
33. Sforza S, Tedeschi T, Corradini R, Ciavardelli D, Dossena A, Marchelli R. Fast solid-phase synthesis of chiral peptide nucleic acid with a high optical purity by a submonomeric strategy. Eur J Org Chem 2003; 1056-63.
34. Seitz O, Kohler O. Convergent strategies for the attachment of fluorescing reporter groups to peptide nucleic acids in solution and on solid phase. Chem-Eur J 2001; 7:3911-25.
35. Nakamura M, Fukunaga Y, Sasa K, Ohtoshi Y, Kanaori K, Hayashi H, et al. 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 2005; 33:5887-95.
36. Marky LA, Breslauer J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 1987; 26:1601-20.
37. Brown SC, Thomson SA, Veal JM, Davis DG. NMR solution structure of a peptide nucleic acid complexed with RNA. Science 1994; 265:777-80.
38. Menchise V, De Simone G, Tedeschi T, Corradini R, Sforza S, Marchelli R, et al. Insights into peptide nucleic acid (PNA) structural features: The crystal structure of a d-lysine-based chiral PNA-DNA duplex.Proc Natl Acad Sci USA 2003; 21:12021-6.
39. Manoharan M, Tivel KL, Zhao M, Nafisi K, Netzel TL. Base-Sequence dependence of emission lifetimes for D141018-30-6NA oligomers and duplexes covalently labeled with pyrene: relative electron-transfer quenching efficiencies of A, G, C and T nucleosides toward pyrene. J Phys Chem 1995; 99:17461-72.
40. Wilson J, Cho Y, Tan S, Cuppoletti A, Kool ET.Quenching of fluorescent nucleobases by neighboring DNA: The "insulator" concept. Chem Bio Chem 2008; 9:279-85.
41. Jacobsen N, Bentzen J, Meldgaard M, Jakobsen MH, Fenger M, Kauppinen S, Skouv J. LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E. Nucleic Acids Res 2002; 30:100.
42. Conlon P, Yang CJ, Wu Chen Y, Martinez K, Kim Y, Stevens N, et al. Pyrene excimer signaling molecular beacons for probing nucleic acids. J Am Chem Soc 2008; 130:336-42.
43. Matsumoto K, Shinohara Y, Bag SS, Takeuchi Y, Morii T, Saito Y, Saito I. Pyrene-labeled deoxyguanosine as a fluorescence sensor to discriminate single and double stranded DNA structures: Design of ends free molecular beacons. Bioorg Med Chem Lett 2009; 19:6392-5.