Increasing the analytical sensitivity by oligonucleotides modified with Para- and Ortho-twisted intercalating nucleic acids - TINA

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Schneider, Uffe V ^a   Géci, Imrich ^b   Jøhnk, Nina ^a   Mikkelsen, Nikolaj D ^a   Pedersen, Erik B ^b   Lisby, Gorm ^a  

^a QuantiBact Inc   (Denmark)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DOUBLE STRANDED DNA; INTERCALATING AGENT; ORTHO TWISTED INTERCALATING NUCLEIC ACID; PARA TWISTED INTERCALATING NUCLEIC ACID; PHOSPHORAMIDOUS ACID; PROTEIN RRS; UNCLASSIFIED DRUG; DNA; OLIGODEOXYRIBONUCLEOTIDE; ORGANOPHOSPHORUS COMPOUND; PRIMER DNA;

ANTIPARALLEL DNA DUPLEX; ARTICLE; BASE MISPAIRING; CHEMICAL MODIFICATION; CONTROLLED STUDY; CROSS REACTION; DNA HELIX; DNA HYBRIDIZATION; DNA STRUCTURE; ESCHERICHIA COLI; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE AMPLIFICATION; IONIC STRENGTH; MELTING POINT; MOLECULAR STABILITY; NONHUMAN; PSEUDOMONAS AERUGINOSA; RRS GENE; SENSITIVITY AND SPECIFICITY; SYNTHESIS; THERMOSTABILITY; BACTERIAL GENE; CHEMISTRY; CONFORMATION; GENETICS; ISOMERISM; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; TRANSITION TEMPERATURE;

ESCHERICHIA COLI; PSEUDOMONAS AERUGINOSA;

DNA; DNA PRIMERS; ESCHERICHIA COLI; GENES, BACTERIAL; INTERCALATING AGENTS; ISOMERISM; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; OLIGODEOXYRIBONUCLEOTIDES; OLIGONUCLEOTIDE PROBES; ORGANOPHOSPHORUS COMPOUNDS; POLYMERASE CHAIN REACTION; TRANSITION TEMPERATURE;

EID: 79958023695     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020565     Document Type: Article

References (23)

1. Egholm M, Buchardt O, Nielsen PE, Berg RH, (1992) Peptide Nucleic-Acids (PNA). Oligonucleotide Analogues with an Achiral Peptide Backbone. J Am Chem Soc 114: 1895-1897.
2. Morita K, Hasegawa C, Kaneko M, Tsutsumi S, Sone J, et al. (2002) 2′-O,4′-C-ethylene-bridged nucleic acids (ENA): Highly nuclease-resistant and thermodynamically stable oligonucleotides for antisense drug. Bioorganic & Medicinal Chemistry Letters 12: 73-76.
3. Obika S, Nanbu D, Hari Y, Morio K, In Y, et al. (1997) Synthesis of 2′-O,4′-C-methyleneuridine and-cytidine. Novel bicyclic nucleosides having a fixed C-3,-endo sugar puckering. Tetrahedron Letters 38: 8735-8738.
4. Singh SK, Nielsen P, Koshkin AA, Wengel J, (1998) LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chemical Communications 455-456.
5. Stirchak EP, Summerton JE, Weller DD, (1989) Uncharged stereoregular nucleic acid analogs: 2. Morpholino nucleoside oligomers with carbamate internucleoside linkages. Nucleic Acids Res 17: 6129-6141.
6. Afonina I, Kutyavin I, Lukhtanov E, Meyer RB, Gamper H, (1996) Sequence-specific arrest of primer extension on single-stranded DNA by an oligonucleotide-minor groove binder conjugate. Proc Natl Acad Sci U S A 93: 3199-3204.
7. Benner SA, Battersby TR, Eschgfaller B, Hutter D, Kodra JT, et al. (1998) Redesigning nucleic acids. Pure and Applied Chemistry 70: 263-266.
8. Matray TJ, Kool ET, (1998) Selective and Stable DNA Base Pairing without Hydrogen Bonds. J Am Chem Soc 120: 6191-6192.
9. Moreau V, Voirin E, Paris C, Kotera M, Nothisen M, et al. (2009) Zip Nucleic Acids: new high affinity oligonucleotides as potent primers for PCR and reverse transcription. Nucleic Acids Research 37: e130.
10. Narayanan S, Gall J, Richert C, (2004) Clamping down on weak terminal base pairs: oligonucleotides with molecular caps as fidelity-enhancing elements at the 5′- and 3′-terminal residues. Nucleic Acids Res 32: 2901-2911.
11. Christensen UB, Pedersen EB, (2002) Intercalating nucleic acids containing insertions of 1-O-(1-pyrenylmethyl)glycerol: stabilisation of dsDNA and discrimination of DNA over RNA. Nucleic Acids Research 30: 4918-4925.
12. Filichev VV, Astakhova IV, Malakhov AD, Korshun VA, Pedersen EB, (2008) 1-, 2-, and 4-ethynylpyrenes in the structure of twisted intercalating nucleic acids: structure, thermal stability, and fluorescence relationship. Chemistry, A European Journal 14: 9968-9980.
13. Géci I, Filichev VV, Pedersen EB, (2006) Synthesis of twisted intercalating nucleic acids possessing acridine derivatives. Thermal stability studies. Bioconjug Chem 17: 950-957.
14. Filichev VV, Pedersen EB, (2005) Stable and selective formation of hoogsteen-type triplexes and duplexes using twisted intercalating nucleic acids (TINA) prepared via postsynthetic Sonogashira solid-phase coupling reactions. J Am Chem Soc 127: 14849-14858.
15. Osman AMA, Jørgensen PT, Bomholt N, Pedersen EB, (2008) Using an aryl phenanthroimidazole moiety as a conjugated flexible intercalator to improve the hybridization efficiency of a triplex-forming oligonucleotide. Bioorganic & Medicinal Chemistry 16: 9937-9947.
16. Filichev VV, Astakhova IV, Malakhov AD, Korshun VA, Pedersen EB, (2008) DNA glue: 1-, 2- and 4-ethynylpyrenes in the structure of twisted intercalating nucleic acids (TINAs), DNA duplexes/triplexes and interstrand excimer formation. Nucleic Acids Symp Ser (Oxf) pp. 347-348.
17. Schneider UV, Severinsen JK, Geci I, Okkels LM, Jøhnk N, et al. (2010) A novel FRET pair for detection of parallel DNA triplexes by the LightCycler. BMC Biotechnol 10: 4.
18. Schneider UV, Mikkelsen ND, Jøhnk N, Okkels LM, Westh H, et al. (2010) Optimal design of parallel triplex forming oligonucleotides containing Twisted Intercalating Nucleic Acids- TINA. Nucleic Acids Res 38: 4394-4403.
19. Fuchs BM, Glöckner FO, Wulf J, Amann R, (2000) Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 66: 3603-3607.
20. Christensen UB, Wamberg M, El-Essawy FA, Ismail A, Nielsen CB, et al. (2004) Intercalating nucleic acids: the influence of linker length and intercalator type on their duplex stabilities. Nucleosides Nucleotides Nucleic Acids 23: 207-225.
21. Cogoi S, Paramasivam M, Filichev V, Geci I, Pedersen EB, et al. (2009) Identification of a new G-quadruplex motif in the KRAS promoter and design of pyrene-modified G4-decoys with antiproliferative activity in pancreatic cancer cells. J Med Chem 52: 564-568.
22. Paramasivam M, Cogoi S, Filichev VV, Bomholt N, Pedersen EB, et al. (2008) Purine twisted-intercalating nucleic acids: a new class of anti-gene molecules resistant to potassium-induced aggregation. Nucleic Acids Res 36: 3494-3507.
23. Hanley BP, Xing L, Cheng RH, (2007) Variance in multiplex suspension array assays: microsphere size variation impact. Theor Biol Med Model 4: 31.