Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure

Abstract

Binding of small oligonucleotides to the periphery of folded RNA can provide insight into the secondary structure of complex RNA in solution. To discriminate between bound and unbound fluorescein-labeled 29-O-methyl RNA probes, we use ionically coated gold nanoparticles to selectively adsorb unbound probes and quench their fluorescence. The target is the 39 untranslated region of Bombyx mori R2 RNA. Fluorescence indicates that R2 sequences complementary to some of the probes are accessible for binding in the three-dimensional structure. Hybridization occurs under homogeneous conditions in the absence of the gold nanoparticles so that steric issues associated with chip-based assays are avoided. The assay is compatible with well plate formats, takes less than 5 min, and requires only 2 pmol or less of unlabeled target RNA per probe sequence tested.

Fluorescent/luminescent detection of natural amino acids by organometallic systems

“…These extraordinary optical features make Au NPs an ideal color reporting group for signaling molecular recognition events and making them function as efficient quenchers for most fluorophores [152][153][154][155][156].…”

Instantaneous Attachment of an Ultrahigh Density of Nonthiolated DNA to Gold Nanoparticles and Its Applications

“…22,23 The generally accepted adsorption model for this process is shown in Figure 1B, where DNA wraps around the AuNP. 22,[24][25][26] The adsorption of non-thiolated DNA has also found important applications in analytical chemistry, [27][28][29][30][31][32][33][34] polymerase chain reactions, 35,36 nanoparticle synthesis, 37,38 and medicine. 37,39 We recently reported that at neutral pH, each 13 nm AuNP adsorbs just around twenty 12-mer DNAs even after overnight incubation, 40 which is consistent with the results from the literature using polyadenosine (e.g A20) as an anchoring block for DNA adsorption with the salt aging approach.…”

Surface Science of DNA Adsorption onto Citrate-Capped Gold Nanoparticles

“…Therefore, AuNPs have been used as a probe for DNA secondary structure and related analytical applications. [25][26][27][28][29][30][31][32] DNA adsorption has also been used to control the growth of AuNPs, 33,34 tune catalytic activities of AuNPs, 35,36 and improve the specificity of polymerase chain reactions (PCR). 37 47 Finally, applications related to drug delivery can also be envisioned.…”