Reduction of Background Generated from Template-Template Hybridizations in the Exponential Amplification Reaction.

The Exponential Amplification Reaction (EXPAR) enables isothermal amplification of nucleic acids. However, applications of EXPAR for the amplification of trace amounts of nucleic acids are hindered by high background. The mechanism of background generation is currently not well understood, although it is assumed to involve nonspecific extension of EXPAR templates by DNA polymerase. We present here a study of the mechanisms of triggering EXPAR background amplification. We show that interactions of EXPAR templates lead to background amplification via polymerase extension of the templates. We further designed and tested two strategies to minimize background amplification: blocking of the 3'-end of the template and sequence-independent weakening of the template-template interactions. Sequence-specific 3'-end blocking showed reduced background, suggesting that 3'-end template interactions are a contributing factor to background amplification. Sequence-independent binding of the whole EXPAR template substantially reduced background amplification by competing with template-template interactions along the entire template sequence. This study provided evidence that nonspecific template interactions and extension by DNA polymerase triggered the amplification of background in EXPAR. The addition of single stranded binding protein to bind nonspecifically with the EXPAR template decreased background by 3 orders of magnitude.

Sequential strand displacement beacon for detection of DNA coverage on functionalized gold nanoparticles.

Functionalizing nanomaterials for diverse analytical, biomedical, and therapeutic applications requires determination of surface coverage (or density) of DNA on nanomaterials. We describe a sequential strand displacement beacon assay that is able to quantify specific DNA sequences conjugated or coconjugated onto gold nanoparticles (AuNPs). Unlike the conventional fluorescence assay that requires the target DNA to be fluorescently labeled, the sequential strand displacement beacon method is able to quantify multiple unlabeled DNA oligonucleotides using a single (universal) strand displacement beacon. This unique feature is achieved by introducing two short unlabeled DNA probes for each specific DNA sequence and by performing sequential DNA strand displacement reactions. Varying the relative amounts of the specific DNA sequences and spacing DNA sequences during their coconjugation onto AuNPs results in different densities of the specific DNA on AuNP, ranging from 90 to 230 DNA molecules per AuNP. Results obtained from our sequential strand displacement beacon assay are consistent with those obtained from the conventional fluorescence assays. However, labeling of DNA with some fluorescent dyes, e.g., tetramethylrhodamine, alters DNA density on AuNP. The strand displacement strategy overcomes this problem by obviating direct labeling of the target DNA. This method has broad potential to facilitate more efficient design and characterization of novel multifunctional materials for diverse applications.