Accelerated photobleaching of a cyanine dye in the presence of a ternary target DNA, PNA probe, dye catalytic complex: a molecular diagnostic

In many settings, molecular testing is needed but unavailable due to complexity and cost. Simple, rapid, and specific DNA detection technologies would provide important alternatives to existing detection methods. Here we report a novel, rapid nucleic acid detection method based on the accelerated photobleaching of the light-sensitive cyanine dye, 3,3'-diethylthiacarbocyanine iodide (DiSC(2)(3) I(-)), in the presence of a target genomic DNA and a complementary peptide nucleic acid (PNA) probe. On the basis of the UV-vis, circular dichroism, and fluorescence spectra of DiSC(2)(3) with PNA-DNA oligomer duplexes and on characterization of a product of photolysis of DiSC(2)(3) I(-), a possible reaction mechanism is proposed. We propose that (1) a novel complex forms between dye, PNA, and DNA, (2) this complex functions as a photosensitizer producing (1)O(2), and (3) the (1)O(2) produced promotes photobleaching of dye molecules in the mixture. Similar cyanine dyes (DiSC(3)(3), DiSC(4)(3), DiSC(5)(3), and DiSC(py)(3)) interact with preformed PNA-DNA oligomer duplexes but do not demonstrate an equivalent accelerated photobleaching effect in the presence of PNA and target genomic DNA. The feasibility of developing molecular diagnostic assays based on the accelerated photobleaching (the smartDNA assay) that results from the novel complex formed between DiSC(2)(3) and PNA-DNA is under way.

The matrix attachment regions (MARs) associated with the Heat Shock Cognate 80 gene ( HSC80) of tomato represent specific regulatory elements

Matrix Attachment Regions (MARs) flank certain plant genes and appear in certain cases to be necessary for their proper regulation. For example, we previously demonstrated that the MARs and introns from the Heat Shock Cognate 80 gene of tomato (HSC80) are necessary for efficient expression of HSC80-based transgenes. MARs may exert their effect by anchoring the ends of a chromatin loop to the nuclear matrix, thereby establishing an independent chromatin domain. Alternatively, MARs may facilitate interactions between activating complexes and DNA. In the first case, MARs should enhance the expression of most genes, while in the latter case, their action might be gene-specific. We addressed this problem by testing whether the HSC80 MARs affected the regulation of an unrelated transgene. We constructed a chimeric transgene composed of the Arabidopsis ADENINE PHOSPHORIBOSYLTRANSFERASE (APT) promoter fused to the maize gene Lc, which encodes a regulator of anthocyanin synthesis, and compared the expression of Lc in Arabidopsis transparent testa glabra (ttg) mutants (which lack anthocyanin pigments) transformed with transgene constructs incorporating the MARs or control DNA fragments that do not bind to the nuclear matrix. Quantitative RT-PCR analysis was used to compare Lc expression in the different transgenic lines. Whether the APT-Lc transgene was flanked by the HSC80 MARs or a control fragment had no effect on expression, while the use of a different MAR, the ARS1 MAR from yeast, significantly decreased expression (P=0.03). Comparison of single-copy and multicopy T-DNA insertions indicated that neither the HSC80 MARs nor the ARS1 MAR could protect the APT-Lc transgene from the negative effect of the integration of multiple copies. In conclusion, this work supports a model in which different regulatory elements within the HSC80 locus interact with the nuclear matrix to induce transcriptional competence.

Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids

Allopolyploid hybridization serves as a major pathway for plant evolution, but in its early stages it is associated with phenotypic and genomic instabilities that are poorly understood. We have investigated allopolyploidization between Arabidopsis thaliana (2n = 2x = 10; n, gametic chromosome number; x, haploid chromosome number) and Cardaminopsis arenosa (2n = 4x = 32). The variable phenotype of the allotetraploids could not be explained by cytological abnormalities. However, we found suppression of 20 of the 700 genes examined by amplified fragment length polymorphism of cDNA. Independent reverse transcription-polymerase chain reaction analyses of 10 of these 20 genes confirmed silencing in three of them, suggesting that approximately 0.4% of the genes in the allotetraploids are silenced. These three silenced genes were characterized. One, called K7, is repeated and similar to transposons. Another is RAP2.1, a member of the large APETALA2 (AP2) gene family, and has a repeated element upstream of its 5' end. The last, L6, is an unknown gene close to ALCOHOL DEHYDROGENASE on chromosome 1. CNG DNA methylation of K7 was less in the allotetraploids than in the parents, and the element varied in copy number. That K7 could be reactivated suggests epigenetic regulation. L6 was methylated in the C. arenosa genome. The present evidence that gene silencing accompanies allopolyploidization opens new avenues to this area of research.