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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

Structure of 8-(1-pentyl-1H-1,2,3-triazole-4-yl)-2′-deoxyadenosine, AT, in which the triazole ring with n-pentyl, added to the normal adenine structure, is shown in grey.
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Figure 1: Structure of 8-(1-pentyl-1H-1,2,3-triazole-4-yl)-2′-deoxyadenosine, AT, in which the triazole ring with n-pentyl, added to the normal adenine structure, is shown in grey.

Mentions: Here we report the synthesis and photophysical characterization of a new fluorescent adenine analogue in DNA, 8-(1-pentyl-1H-1,2,3-triazole-4-yl)-2′-deoxyadenosine (AT) (Figure 1), which shows promising features compared to other fluorescent adenine analogues such as the commercially available 2-aminopurine. In a previous investigation, several adenosine derivatives of AT were studied and shown to exhibit a very high-quantum yield in THF and red-shifted absorption relative to the DNA absorption band. One of the compounds, having an isopentyl substituent in the triazole ring, showed a very high-quantum yield in both THF (0.62) and water (>0.50) (49). In this work, we characterize the 2′-deoxyadenosine form of AT both in methanol and water. In addition, we have incorporated it into 10 different 10-mer oligonucleotides with various base-stacking environments in order to perform a photophysical and structural characterization of AT in DNA. We find that AT causes only minor perturbations to natural B-DNA. Furthermore, quantum yields for AT incorporated into single- and double-stranded DNA reach maximum values that far exceed corresponding values for 2-aminopurine. Moreover, we have investigated the base-pairing specificity of AT with all four natural DNA-bases. To our surprise, we find that AT forms equally stable base pairs with thymine and adenine. In conclusion, AT is a very promising new fluorescent base analogue, showing high sensitivity to its microenvironment.Figure 1.


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)

Structure of 8-(1-pentyl-1H-1,2,3-triazole-4-yl)-2′-deoxyadenosine, AT, in which the triazole ring with n-pentyl, added to the normal adenine structure, is shown in grey.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Structure of 8-(1-pentyl-1H-1,2,3-triazole-4-yl)-2′-deoxyadenosine, AT, in which the triazole ring with n-pentyl, added to the normal adenine structure, is shown in grey.
Mentions: Here we report the synthesis and photophysical characterization of a new fluorescent adenine analogue in DNA, 8-(1-pentyl-1H-1,2,3-triazole-4-yl)-2′-deoxyadenosine (AT) (Figure 1), which shows promising features compared to other fluorescent adenine analogues such as the commercially available 2-aminopurine. In a previous investigation, several adenosine derivatives of AT were studied and shown to exhibit a very high-quantum yield in THF and red-shifted absorption relative to the DNA absorption band. One of the compounds, having an isopentyl substituent in the triazole ring, showed a very high-quantum yield in both THF (0.62) and water (>0.50) (49). In this work, we characterize the 2′-deoxyadenosine form of AT both in methanol and water. In addition, we have incorporated it into 10 different 10-mer oligonucleotides with various base-stacking environments in order to perform a photophysical and structural characterization of AT in DNA. We find that AT causes only minor perturbations to natural B-DNA. Furthermore, quantum yields for AT incorporated into single- and double-stranded DNA reach maximum values that far exceed corresponding values for 2-aminopurine. Moreover, we have investigated the base-pairing specificity of AT with all four natural DNA-bases. To our surprise, we find that AT forms equally stable base pairs with thymine and adenine. In conclusion, AT is a very promising new fluorescent base analogue, showing high sensitivity to its microenvironment.Figure 1.

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