Complementary Oligonucleotide Conjugated Multicolor Carbon Dots for Intracellular Recognition of Biological Events

Abstract

By using complementary DNA sequences as surface ligands, we selectively allow two individual diffusing “dual-color” carbon dots to interact in situ and in vitro. Spontaneous nanoscale oxidation of surface-abundant nitroso-/nitro-functionalities leads to two distinctly colored carbon dots (CD) which are isolated by polarity driven chromatographic separation. Green- and red-emitting carbon dots (gCD and rCD) were decorated by complementary single-stranded DNAs which produce a marked increase in the fluorescence emission of the respective carbon dots. Mutual colloidal interactions are achieved through hybridization of complementary DNA base pairs attached to the respective particles, resulting in quenching of their photoluminescence. The observed post-hybridization quenching is presumably due to a combined effect from an aggregation of CDs post duplex DNA formation and close proximity of multicolored CDs, having overlapped spectral regions leading to a nonradiative energy transfer process possibly released as heat. This strategy may contribute to the rational design of mutually interacting carbon dots for a better control over the resulting assembly structure for studying different biological phenomenon including molecular cytogenetics. One of the newly synthesized CDs was successfully used to image intracellular location of GAPDH mRNA using an event of change in fluorescence intensity (FI) of CDs. This selectivity was introduced by conjugating an oligonucleotide harboring complementary sequence to GAPDH mRNA. FI of this conjugated carbon dot, rCD-GAPDH, was also found to decrease in the presence of Ca2+, varied in relation to H+ concentrations, and could serve as a tool to quantify the intracellular concentrations of Ca2+ and pH value (H+) which can give important information about cell survival. Therefore, CD-oligonucleotide conjugates could serve as efficient probes for cellular events and interventions.

Probing the mutation independent interaction of DNA probes with SARS-CoV-2 variants through a combination of surface-enhanced Raman scattering and machine learning

“…An insignificant increase in absorbance with no change in FWHM was observed when Au-ASO NPs were added with SARS-CoV-2 negative RNAs. This change in surface plasmon band of AuNPs indicated the successful aggregation of Au-ASO NPs only in presence of their target RNAs( Moitra et al, 2020 ; Ostadhossein et al, 2020 ; Rump et al, 2010 ; Srivastava et al, 2020 ). It was also observed that the mixture of N-ASO1 and N-ASO2 gave a better aggregation response than the mixture having N-ASO3 and N-ASO4 ( Fig.…”

A rapid RNA extraction-free lateral flow assay for molecular point-of-care detection of SARS-CoV-2 augmented by chemical probes

“…All the ASOs after conjugation were purified by sephadex G-25 column ( Fig. S1 ) using RNase free water as eluent to remove unbounded FAM and biotin ( Ostadhossein et al, 2020 ; Srivastava et al, 2020 ). It was observed that under identical condition, the purified fraction of ASO2 conjugated with 6-FAM (ASO2-F) showed increased absorbance at 480 nm ( Fig.…”

Carbon quantum dots for the detection of antibiotics and pesticides

“…The ease of preparation and modification of CQDs offers advantages not only in fine-tuning of their electronic and optical properties but also mediation of the interaction between CQDs and analytes leading to fluorescence quenching or enhancement. Due to the diverse surface structure of CQDs, they are known to be able to interact with many compounds and biomolecules via a variety of intermolecular interactions [8][9][10][11]. Examples include oligonucleotides (electrostatic, hydrogen bonding, and p-p stacking interaction), proteins (electrostatic, hydrogen bonding, and hydrophobic interaction), and metal ions (hard-soft acid-base (HSAB) interactions).…”