Nucleic acid sensing by regenerable surface-associated isothermal rolling circle amplification

A novel method for regenerating biosensors has been developed in which the highly specific detection of nucleic acid sequences is carried out using molecular padlock probe (MPP) technology and surface-associated rolling circle amplification (RCA). This technique has a low occurrence of false positive results when compared to polymerase chain reaction, and is an isothermal reaction, which is advantageous in systems requiring low power consumption such as remote field sensing applications. Gold-sputtered 96-well polystyrene microplates and a fluorescent label were used to explore the detection limits of the surface-associated RCA technique, specificity for different MPP, conditions for regeneration of the biomolecular sensing surface, and reproducibility of measurements on regenerated surfaces. The technique was used to create highly selective biomolecular surfaces capable of discriminating between DNA oligonucleotides with sequences identical to RNA from infectious salmon anemia (ISA) and infectious hematopoietic necrosis (IHN) virus. As little as 0.6 fmol of circularized MPP was detectable with this fluorimetric assay. The sensing layers could be reused for at least four cycles of amplification using thermal denaturation, with less than 33% decrease in RCA response over time. Because the nucleic acid product of the test is attached to a surface during amplification, the technique is directly applicable to a variety of existing sensing platforms, including acoustic wave and optical devices.

Detection and identification of IHN and ISA viruses by isothermal DNA amplification in microcapillary tubes

Unique base sequences derived from RNA of both infectious hematopoietic necrosis virus (IHNV) and infectious salmon anemia virus (ISAV) were detected and identified using a combination of surface-associated molecular padlock DNA probes (MPPs) and rolling circle amplification (RCA) in microcapillary tubes. DNA oligonucleotides with base sequences identical to RNA obtained from IHNV or ISAV were recognized by MPPs. Circularized MPPs were then captured on the inner surfaces of glass microcapillary tubes by immobilized DNA oligonucleotide primers. Extension of the immobilized primers by isothermal RCA produced DNA concatamers, which were labeled with fluorescent SYBR Green II nucleic acid stain, and measured by microfluorimetry. Molecular padlock probes, combined with this method of surface-associated isothermal RCA, exhibited high selectivity without the need for thermal cycling. This method is applicable to the design of low-power field sensors capable of multiplex detection of viral, bacterial, and protozoan pathogens within localized regions of microcapillary tubes.

Detection of infectious haematopoietic necrosis virus and infectious salmon anaemia virus by molecular padlock amplification

A new method for the molecular detection of the fish pathogens, infectious haematopoietic necrosis virus (IHNV) and infectious salmon anaemia virus (ISAV), is described. By employing molecular padlock probe (MPP) technology combined with rolling circle amplification (RCA) and hyperbranching (Hbr), it is possible to detect RNA target sequence from these viruses at levels comparable with those detected by the polymerase chain reaction (PCR), but without prior reverse transcription. The use of MPP technology combined with RCA and Hbr for the detection of IHNV and ISAV in fish exhibited selectivity comparable with that of PCR while potentially reducing the time and cost required for analysis. The method described was used to detect as few as 10(4) DNA oligonucleotide targets and was sequence-specific at the single base level. Viral RNA could be detected directly, either alone or in the presence of non-viral RNA from fish tissue. This technology is applicable for detecting a variety of microbes, in addition to IHNV and ISAV, and is ideal for further integration into a biosensor platform for on-site diagnosis of pathogen infection in fish.

Monoclonal antibodies show that kinase C phosphorylation of GAP-43 during axonogenesis is both spatially and temporally restricted in vivo

To study the role of kinase C phosphorylation in the distribution and function of GAP-43 we have generated a panel of mAbs that distinguish between GAP-43 that has been phosphorylated by kinase C and forms that have not. One class of antibodies, typified by 2G12/C7, reacts with only the phosphorylated form of GAP-43; it recognizes the peptide IQAS(PO4)FR equivalent to residues 38-43 that includes the single kinase C phosphorylation site at serine. Another, exemplified by 10E8/E7, reacts with both phosphorylated and nonphosphorylated forms. We have used the antibodies to study the distribution of kinase C-phosphorylated GAP-43 during axonogenesis and in the adult nervous system. Two major findings emerge. First, there is a lag between the initiation of axon outgrowth and the phosphorylation of GAP-43 by kinase C. The extent of this lag period varies between the different structures studied. In some cases, e.g., the trigeminal nerve, our result suggest that kinase C phosphorylation may be correlated with proximity of the growing axon to its target. Second, kinase C-phosphorylated GAP-43 is always spatially restricted to the distal axon. It is never seen either proximally or in cell bodies, even those with high levels of GAP-43 protein. This result also implies that GAP-43 is axonally transported in the non-kinase C phosphorylated form. Thus, kinase C phosphorylation of GAP-43 is not required for axon outgrowth or growth cone function per se and may be more related to interactions of the growth cone with its environment.