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Characterization of photophysical and base-mimicking properties of a novel fluorescent adenine analogue in DNA.

Dierckx A, Dinér P, El-Sagheer AH, Kumar JD, Brown T, Grøtli M, Wilhelmsson LM - Nucleic Acids Res. (2011)

Bottom Line: To increase the diversity of fluorescent base analogues with improved properties, we here present the straightforward click-chemistry-based synthesis of a novel fluorescent adenine-analogue triazole adenine (A(T)) and its photophysical characterization inside DNA.A(T) shows promising properties compared to the widely used adenine analogue 2-aminopurine.In conclusion, A(T) shows strong potential as a new fluorescent adenine analogue for monitoring changes within its microenvironment in DNA.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, University of Gothenburg, S-41296 Gothenburg, Sweden.

ABSTRACT
To increase the diversity of fluorescent base analogues with improved properties, we here present the straightforward click-chemistry-based synthesis of a novel fluorescent adenine-analogue triazole adenine (A(T)) and its photophysical characterization inside DNA. A(T) shows promising properties compared to the widely used adenine analogue 2-aminopurine. Quantum yields reach >20% and >5% in single- and double-stranded DNA, respectively, and show dependence on neighbouring bases. Moreover, A(T) shows only a minor destabilization of DNA duplexes, comparable to 2-aminopurine, and circular dichroism investigations suggest that A(T) only causes minimal structural perturbations to normal B-DNA. Furthermore, we find that A(T) shows favourable base-pairing properties with thymine and more surprisingly also with normal adenine. In conclusion, A(T) shows strong potential as a new fluorescent adenine analogue for monitoring changes within its microenvironment in DNA.

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Related in: MedlinePlus

(a) Br2/NaOAc-buffer, r.t., overnight, 81%. (b) Pd(PPh3)4 (4 mol%), CuI (8 mol%), TMS-acetylene, Amberlite IRA-67, THF, 40°C, 2 h, 91%. (c) (i) DMTrCl, pyridine, overnight, r.t.; (ii) NH3 (25% aq.), 2 h 65%. (d) (i) Pentylbromide, NaN3, water, 140°C, 1 h; (ii) CuI, ethyl acetate, 14 h, r.t., 76%. (e) (i) TMSCl, pyridine, 2 h; (ii) BzCl, 3 h; (iii) Water, 15 min then NH3 (aq.), 30 min, 68%. (f) DIPEA (0.11 ml, 0.64 mmol), 2-Cyanoethyl-N,N-diisopropylchlorophosphoramidite, DCM, 1 h, 91%. (g) Acetic acid, 30 min, 34%.
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SCH1: (a) Br2/NaOAc-buffer, r.t., overnight, 81%. (b) Pd(PPh3)4 (4 mol%), CuI (8 mol%), TMS-acetylene, Amberlite IRA-67, THF, 40°C, 2 h, 91%. (c) (i) DMTrCl, pyridine, overnight, r.t.; (ii) NH3 (25% aq.), 2 h 65%. (d) (i) Pentylbromide, NaN3, water, 140°C, 1 h; (ii) CuI, ethyl acetate, 14 h, r.t., 76%. (e) (i) TMSCl, pyridine, 2 h; (ii) BzCl, 3 h; (iii) Water, 15 min then NH3 (aq.), 30 min, 68%. (f) DIPEA (0.11 ml, 0.64 mmol), 2-Cyanoethyl-N,N-diisopropylchlorophosphoramidite, DCM, 1 h, 91%. (g) Acetic acid, 30 min, 34%.


Characterization of photophysical and base-mimicking properties of a novel fluorescent adenine analogue in DNA.

Dierckx A, Dinér P, El-Sagheer AH, Kumar JD, Brown T, Grøtli M, Wilhelmsson LM - Nucleic Acids Res. (2011)

(a) Br2/NaOAc-buffer, r.t., overnight, 81%. (b) Pd(PPh3)4 (4 mol%), CuI (8 mol%), TMS-acetylene, Amberlite IRA-67, THF, 40°C, 2 h, 91%. (c) (i) DMTrCl, pyridine, overnight, r.t.; (ii) NH3 (25% aq.), 2 h 65%. (d) (i) Pentylbromide, NaN3, water, 140°C, 1 h; (ii) CuI, ethyl acetate, 14 h, r.t., 76%. (e) (i) TMSCl, pyridine, 2 h; (ii) BzCl, 3 h; (iii) Water, 15 min then NH3 (aq.), 30 min, 68%. (f) DIPEA (0.11 ml, 0.64 mmol), 2-Cyanoethyl-N,N-diisopropylchlorophosphoramidite, DCM, 1 h, 91%. (g) Acetic acid, 30 min, 34%.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105426&req=5

SCH1: (a) Br2/NaOAc-buffer, r.t., overnight, 81%. (b) Pd(PPh3)4 (4 mol%), CuI (8 mol%), TMS-acetylene, Amberlite IRA-67, THF, 40°C, 2 h, 91%. (c) (i) DMTrCl, pyridine, overnight, r.t.; (ii) NH3 (25% aq.), 2 h 65%. (d) (i) Pentylbromide, NaN3, water, 140°C, 1 h; (ii) CuI, ethyl acetate, 14 h, r.t., 76%. (e) (i) TMSCl, pyridine, 2 h; (ii) BzCl, 3 h; (iii) Water, 15 min then NH3 (aq.), 30 min, 68%. (f) DIPEA (0.11 ml, 0.64 mmol), 2-Cyanoethyl-N,N-diisopropylchlorophosphoramidite, DCM, 1 h, 91%. (g) Acetic acid, 30 min, 34%.
Bottom Line: To increase the diversity of fluorescent base analogues with improved properties, we here present the straightforward click-chemistry-based synthesis of a novel fluorescent adenine-analogue triazole adenine (A(T)) and its photophysical characterization inside DNA.A(T) shows promising properties compared to the widely used adenine analogue 2-aminopurine.In conclusion, A(T) shows strong potential as a new fluorescent adenine analogue for monitoring changes within its microenvironment in DNA.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, University of Gothenburg, S-41296 Gothenburg, Sweden.

ABSTRACT
To increase the diversity of fluorescent base analogues with improved properties, we here present the straightforward click-chemistry-based synthesis of a novel fluorescent adenine-analogue triazole adenine (A(T)) and its photophysical characterization inside DNA. A(T) shows promising properties compared to the widely used adenine analogue 2-aminopurine. Quantum yields reach >20% and >5% in single- and double-stranded DNA, respectively, and show dependence on neighbouring bases. Moreover, A(T) shows only a minor destabilization of DNA duplexes, comparable to 2-aminopurine, and circular dichroism investigations suggest that A(T) only causes minimal structural perturbations to normal B-DNA. Furthermore, we find that A(T) shows favourable base-pairing properties with thymine and more surprisingly also with normal adenine. In conclusion, A(T) shows strong potential as a new fluorescent adenine analogue for monitoring changes within its microenvironment in DNA.

Show MeSH
Related in: MedlinePlus