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Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design.

Foller Larsen A, Dumat B, Wranne MS, Lawson CP, Preus S, Bood M, Gradén H, Wilhelmsson LM, Grøtli M - Sci Rep (2015)

Bottom Line: We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations.TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives.This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.

View Article: PubMed Central - PubMed

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

ABSTRACT
Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (εΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.

No MeSH data available.


Structures of adenine, the quadracyclic adenine analogues qA and qAN1-4, and the new series of adenine analogues (3).
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f1: Structures of adenine, the quadracyclic adenine analogues qA and qAN1-4, and the new series of adenine analogues (3).

Mentions: The major challenge when designing bright, non-perturbing FBAs is that their size must be kept small in order to minimize potential adverse effects on nucleic acid structure and function whilst retaining base-pairing ability. This requirement makes it challenging to substantially modulate the optical properties of non-perturbing FBAs. The challenge is further enhanced by the often not satisfactorily understood relationship between chemical structure and optical properties. While some general rules of thumb exist for designing fluorescent molecules, the development of probes with improved properties still relies almost exclusively on empirical approaches. Hammett constant correlations, sometimes in combination with DFT calculations, have previously been used to rationalize the design of fluorescent molecules as well as to tune the emission wavelengths or optimize the fluorescence quantum yields28293031. These approaches are, however, limited to fluorophores bearing substituted phenyl moieties and are not applicable in more general cases. Our approach has been to use TDDFT calculations with the B3LYP functional and it has been proven to accurately predict the three lowest singlet transition energies of the tricyclic cytosine family323334. This method was recently and successfully used to develop four microenvironment sensitive analogues of quadracyclic adenine (qA, Fig. 1, 1)35, the qAN-family (2), which were synthesized via an efficient 2-step pathway from a common intermediate36. Interestingly, the relative quantum yields values of the four qANs and qA were well described by the calculated oscillator strength values.


Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design.

Foller Larsen A, Dumat B, Wranne MS, Lawson CP, Preus S, Bood M, Gradén H, Wilhelmsson LM, Grøtli M - Sci Rep (2015)

Structures of adenine, the quadracyclic adenine analogues qA and qAN1-4, and the new series of adenine analogues (3).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4530663&req=5

f1: Structures of adenine, the quadracyclic adenine analogues qA and qAN1-4, and the new series of adenine analogues (3).
Mentions: The major challenge when designing bright, non-perturbing FBAs is that their size must be kept small in order to minimize potential adverse effects on nucleic acid structure and function whilst retaining base-pairing ability. This requirement makes it challenging to substantially modulate the optical properties of non-perturbing FBAs. The challenge is further enhanced by the often not satisfactorily understood relationship between chemical structure and optical properties. While some general rules of thumb exist for designing fluorescent molecules, the development of probes with improved properties still relies almost exclusively on empirical approaches. Hammett constant correlations, sometimes in combination with DFT calculations, have previously been used to rationalize the design of fluorescent molecules as well as to tune the emission wavelengths or optimize the fluorescence quantum yields28293031. These approaches are, however, limited to fluorophores bearing substituted phenyl moieties and are not applicable in more general cases. Our approach has been to use TDDFT calculations with the B3LYP functional and it has been proven to accurately predict the three lowest singlet transition energies of the tricyclic cytosine family323334. This method was recently and successfully used to develop four microenvironment sensitive analogues of quadracyclic adenine (qA, Fig. 1, 1)35, the qAN-family (2), which were synthesized via an efficient 2-step pathway from a common intermediate36. Interestingly, the relative quantum yields values of the four qANs and qA were well described by the calculated oscillator strength values.

Bottom Line: We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations.TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives.This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.

View Article: PubMed Central - PubMed

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

ABSTRACT
Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (εΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.

No MeSH data available.