Dual fluorescent deoxyguanosine mimics for FRET detection of G-quadruplex folding

Abstract

Replacement of deoxyguanosine (dG) nucleobases within G-tetrads of G-quadruplex folding oligonucleotides with donor (D)/acceptor (A) fluorescent 8aryldG residues provides diagnostic FRET signalling for G-quadruplex detection.

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

“…8-Furyl-dG in the syn positions of 10 and 14 elevated T m of TBA GQ, while the more lipophilic benzothienyl derivative decreased it slightly in the syn G5 position and more extensively in the anti G6 position. Double labeling with furyl and benzothienyl derivatives enhanced the destabilization when one of the analogs was in anti position; however, when both probes substituted for syn dG positions, the wild type was significantly stabilized [ 112 ]. The push-pull phenomenon in the TBA GQ was also studied with acetylphenyl, benzo[b]thienyl, quinolyl, pyren-1-yl ( Figure 8 , 7 ), and the 8-vinyl tethered derivatives of acetylphenyl and benzo[b]thienyl attached to C8 of dG ( Figure 8 ).…”

C-Linked 8-aryl guanine nucleobase adducts: biological outcomes and utility as fluorescent probes

“…Thus, 8arylG probes can be effective diagnostic tools in duplex–GQ exchange systems that are commonly employed in DNA-based detection strategies. 42 , 52 , 53 The level of precision offered by internal fluorescent nucleobase mimics can complement other approaches including end-labelled dyes and label-free dyes, because the internal probes may assist in establishing Gs in the tetrad versus loop positions, site(s) of ligand binding, and remove false negatives or positives that can occur with the use of external dyes that are not covalently attached to the aptamer. 101 …”

“…10a ). 53 This prompted the synthesis of 8-vinyl-benzo[ b ]thienyl-dG (vBthG, Fig. 10b ), which has an absorbance maxima at ∼380 nm and will yield effective spectral overlap with the emission of FurG.…”

“…As a result, C-linked aryl moieties extend the purine π-system, which commonly results in fluorescent nucleobase analogues. 9 – 11 Emissive DNA bases enjoy a wide range of applications that include reporters of nucleic acid structure and function; 38 – 43 detectors of nucleobase damage, single nucleotide polymorphisms (SNPs) and mismatch dynamics; 44 – 46 probes for understanding protein–DNA interactions; 47 – 50 components of aptamers to provide a fluorescent signal upon target binding; 51 – 53 and oligonucleotide-based therapeutics. 54 …”

“… 60 – 63 In antiparallel GQs, 8arylGs also behave as ideal fluorescent probes, exhibiting emission that is sensitive to GQ folding. 38 , 42 , 52 , 53 …”