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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

CD spectra of all 10 DNA duplexes containing the AT analogue. Duplexes are denoted by the bases neighbouring AT and consist of the modified strands GA (black), CT (red), GC (dark blue), CA (brown), GG (purple), CC (orange), TA (light blue), AA (grey), AC (pink) and TG (green) hybridized to the complementary natural DNA strand. Spectra were recorded in phosphate buffer (500 mM Na+, pH 7.5) at 25°C at a duplex concentration of 2.5 µM.
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Figure 4: CD spectra of all 10 DNA duplexes containing the AT analogue. Duplexes are denoted by the bases neighbouring AT and consist of the modified strands GA (black), CT (red), GC (dark blue), CA (brown), GG (purple), CC (orange), TA (light blue), AA (grey), AC (pink) and TG (green) hybridized to the complementary natural DNA strand. Spectra were recorded in phosphate buffer (500 mM Na+, pH 7.5) at 25°C at a duplex concentration of 2.5 µM.

Mentions: The CD spectra that were recorded for the duplexes, consisting of a modified strand containing one AT (Table 1) and its unmodified complementary sequence are presented in Figure 4. Analysis of the spectra between 200 and 300 nm shows a high resemblance to the CD signature of a natural B-DNA-helix, which is characterized by a positive band at 275 nm, a negative band at 240 nm, a band which is less negative or positive at 220 nm and a narrow negative band in the region between 220 and 190 nm, preceded by a large positive peak at 180–190 nm. Some modified duplexes show an almost identical CD-spectrum to their natural DNA (CT, CA, TG, CC and AA) (Supplementary Data S2), whereas others show more distinct differences between the corresponding spectra (strands GA, GC, GG, TA and AC) (Supplementary Data S2). Sequences GA, GC and GG, having a guanine flanking AT at the 5′-side, show the most perturbed CD signals. As an illustration of this variation, one of the latter spectra (GG) is shown in Figure 5 and compared to the CD spectrum of the corresponding unmodified helix and to the absorption difference between the modified and natural duplex of this sequence. The resulting differential absorption band correlates well to the regions (∼210, 230 and 295 nm) where the CD-spectra of natural and modified duplexes differ most significantly (Figure 5).Figure 4.


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)

CD spectra of all 10 DNA duplexes containing the AT analogue. Duplexes are denoted by the bases neighbouring AT and consist of the modified strands GA (black), CT (red), GC (dark blue), CA (brown), GG (purple), CC (orange), TA (light blue), AA (grey), AC (pink) and TG (green) hybridized to the complementary natural DNA strand. Spectra were recorded in phosphate buffer (500 mM Na+, pH 7.5) at 25°C at a duplex concentration of 2.5 µM.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: CD spectra of all 10 DNA duplexes containing the AT analogue. Duplexes are denoted by the bases neighbouring AT and consist of the modified strands GA (black), CT (red), GC (dark blue), CA (brown), GG (purple), CC (orange), TA (light blue), AA (grey), AC (pink) and TG (green) hybridized to the complementary natural DNA strand. Spectra were recorded in phosphate buffer (500 mM Na+, pH 7.5) at 25°C at a duplex concentration of 2.5 µM.
Mentions: The CD spectra that were recorded for the duplexes, consisting of a modified strand containing one AT (Table 1) and its unmodified complementary sequence are presented in Figure 4. Analysis of the spectra between 200 and 300 nm shows a high resemblance to the CD signature of a natural B-DNA-helix, which is characterized by a positive band at 275 nm, a negative band at 240 nm, a band which is less negative or positive at 220 nm and a narrow negative band in the region between 220 and 190 nm, preceded by a large positive peak at 180–190 nm. Some modified duplexes show an almost identical CD-spectrum to their natural DNA (CT, CA, TG, CC and AA) (Supplementary Data S2), whereas others show more distinct differences between the corresponding spectra (strands GA, GC, GG, TA and AC) (Supplementary Data S2). Sequences GA, GC and GG, having a guanine flanking AT at the 5′-side, show the most perturbed CD signals. As an illustration of this variation, one of the latter spectra (GG) is shown in Figure 5 and compared to the CD spectrum of the corresponding unmodified helix and to the absorption difference between the modified and natural duplex of this sequence. The resulting differential absorption band correlates well to the regions (∼210, 230 and 295 nm) where the CD-spectra of natural and modified duplexes differ most significantly (Figure 5).Figure 4.

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