Ligase chain reaction (LCR) offers a simple and robust alternative platform for nucleic acid amplification, but its application has been limited because the LCR products are mostly detected by gel electrophoresis separation or heterogeneous analysis. In this paper, we report a novel homogeneous LCR assay by using cationic conjugated polymers (CCPs) as an indicator for detection of single-nucleotide polymorphism (SNP). For LCR, we design two pairs of unique target-complement probes. Each pair of probes contains two adjacent probes, in which one probe is designed with phosphorothioate modification at its 3'-end, and the other probe is labeled with fluorescein at its 5'-end. After the LCR, the two adjacent probes are ligated to form one DNA strand with a fluorescein label at its 5'-end and phosphorothioate modification at its 3'-end, which is resistant to the exonuclease I and exonuclease III degradation. When the CCP is added, because of the strong electrostatic interactions between CCP and DNA, effective fluorescence resonance energy transfer (FRET) from the CCP to the fluorescein-labeled DNA can be observed. In contrast, the unligated fluorescein-labeled probes are degraded to the mononucleotides by exonuclease I and exonuclease III. Introduction of CCP leads to inefficient FRET results because much weaker electrostatic interactions between the fluorescein-labeled mononucleotides and CCP keep the fluorescein far away from CCP. Accordingly, homogeneous LCR for SNP detection is performed successfully. The method is sensitive and specific enough to detect 1 fM (600 zmol) DNA molecules. It is possible to quantify SNP and accurately determine the allele frequency as low as 1.0%. This proposed assay strategy extends the application of LCR and provides a new platform for homogeneous detection of SNP.
A novel, homogeneous and sensitive assay for the detection of single nucleotide polymorphisms (SNPs) by integration of rolling circle amplification (RCA) and cationic conjugated polymer (CCP) has been developed and tested. Mutant DNA serves as the template for specifically circularizing a padlock probe (PLP) with a sequence that is complementary to the mutant DNA. Afterwards, the mutant DNA directly acts as the primer to initiate the RCA reaction in the presence of phi29 DNA polymerase that generates a long, tandem single-strand DNA product. During the RCA reaction, fluorescein-labeled dUTPs are incorporated into the RCA products. When the CCP is introduced, efficient FRET from CCP to fluorescein occurs as a result of the strong electrostatic interactions between the CCP and the DNA produced by RCA. The wild-type DNA contains a single base mismatch with PLP with the result that the PLP is not circularized, RCA is not triggered and inefficient FRET results. By measuring the change of the emission intensities of CCP and fluorescein, it was possible to detect the SNP in a homogeneous manner. The method is sensitive and specific enough to detect 0.1 pmol/L mutant DNA and to determine a mutant allele frequency as low as 2.0%. Single-nucleotide polymorphisms (SNPs) are the most common type of genetic variation. Cationic conjugated polymers (CCPs) with a large number of repeated absorbing units can transfer the excitation energy along the whole CCP backbone to the chromophore reporter [12]. Because of their unique light-harvesting properties, CCPs provide an effective platform for homogeneous SNP detection based on the formation of polyelectrolyte complexes stabilized by electrostatic interactions between the CCPs and negatively charged DNA. When a fluorophore-labeled nucleotide is incorporated into the DNA chain during the primer extension reaction at an SNP
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