Positively Charged Compact Quantum Dot–DNA Complexes for Detection of Nucleic Acids

Abstract

Novel QD-DNA complexes are prepared by simple electrostatic interaction between pegylated amine-functionalized CdSe/ZnS quantum dots (QDs) and DNA. The cationic nature of the amine functionality on the QD surface allows for formation of an electrostatic complex with negatively charged DNA. The presence of polyethylene glycol (PEG5000) molecules on the QD leads to enhanced stability and decreased nonspecific adsorption of DNA on the QD surface. Unlike assembly of QD-DNA based on hydrogen bonding, the present QD probes tend to be more strongly stabilized during the hybridization process by increasing the overall negative charges. In addition, the DNA loading efficiency can be modulated by changing the pH of the reaction medium. The fluorescence of the QD is quenched up to 90% by complexation with 5'-TAMRA-modified oligonucleotide (TAMRA=carboxytetramethylrhodamine) through fluorescence resonance energy transfer (FRET). With the FRET pair we selected, the R(0) value was calculated to be 5.5 nm and r is about 5 nm. This quenching of QD fluorescence is then reversed on binding of unlabeled target DNA. The maximum recovery of QD fluorescence is 60%. The QD-DNA probe (5DNA/QD) exhibits selective photoluminescence (PL) recovery in the presence of target oligonucleotide with a PL ratio of 3 for complementary versus noncomplementary. The present QD-DNA probes also show the capability to detect the synthetic 100-mer oligonucleotide derived from H5N1 influenza virus when present at concentrations as low as 200 nM in the solution.