Quadracyclic Adenine: A Non-Perturbing Fluorescent Adenine Analogue
Artikel i vetenskaplig tidskrift, 2012

Fluorescent-base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base-pairing properties of a new environment-sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid-phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B-form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2-aminopurine, and the recently developed triazole adenine, qA shows highly specific base-pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300 nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8?% with an emission maximum at 456 nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2-aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid-containing systems.

duplex stability

peptide nucleic-acid

binding

oligonucleotides

pteridine nucleoside analogs

dna-base analog

fluorescent

form

DNA solid-phase synthesis

size-expanded dna

duplexes

DNA

2-aminopurine

fluorescence

complex-formation

Författare

Anke Dierckx

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

Francois-Alexandre Miannay

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

N. Gaied

University of Southampton

S. Preus

Kobenhavns Universitet

Markus Björck

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

T. Brown

University of Southampton

Marcus Wilhelmsson

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

Chemistry - A European Journal

0947-6539 (ISSN) 1521-3765 (eISSN)

Vol. 18 5987-5997

Styrkeområden

Nanovetenskap och nanoteknik

Livsvetenskaper och teknik

Ämneskategorier

Fysikalisk kemi

Biofysik

Kemi

DOI

10.1002/chem.201103419