A molecular beacon biosensor for viral RNA detection based on HyCaSD strategy.

In the present study, a molecular beacon biosensor was developed to enable efficient detection of the viral RNAs using a previously described HyCaSD platform. The HyCaSD molecular beacon probes were labeled with the Cy5 and BHQ3 at each end of the hairpin probes. The fluorescent signal was detected immediately only when the molecular beacon probes specifically hybridized to the target sequence and unfolded their hairpin structures. This combination greatly improved the sensitivity with LOD of 100 copy equivalents per reaction (around 20-fold greater than the original HyCaSD). In addition, our MB-based HyCaSD demonstrated a single-step, single-tube and actual-time RNA detection procedure, thereby bringing it a major step closer to point-of-care diagnostic applications for viral infectious diseases.

Hybridization Cascade Plus Strand-Displacement Isothermal Amplification of RNA Target with Secondary Structure Motifs and Its Application for Detecting Dengue and Zika Viruses.

Biological RNA generally comprises secondary structure motifs which cause a problem for target RNA detection by isothermal amplification methods. The complexity of the secondary structures makes RNA targets inaccessible for probe hybridization, resulting in decreased sensitivity and selectivity. This is particularly important because the hybridization step of the isothermal amplification method requires a limited temperature range. A strand-displacement strategy can enhance the hybridization efficiency between the probe and target RNA with secondary structure motifs. A short, single-stranded segment within the secondary structure can be used as a toehold for initiating strand displacement. The strategy has been used to establish a highly sensitive isothermal amplification by a combination of a hairpin probe hybridization and strand-displacement amplification. The hairpin probe is placed on the single-stranded segment of the target RNA's secondary structure to initiate strand displacement. The probe's hybridization cascade provides a template for exponential amplification in two directions by strand-displacement amplification, designated hybridization cascade plus strand-displacement isothermal amplification (HyCaSD). The method requires no reverse transcription step. HyCaSD showed an excellent sensitivity with the limit of detection in the femtomolar (fM) range for synthetic targets as well as viral RNAs. Discrimination between DENV/ZIKV and JEV/CHIKV was successfully demonstrated using real viruses. Therefore, HyCaSD is a promising platform that can be further developed for diagnostic applications.

Streptavidin aptamers: affinity tags for the study of RNAs and ribonucleoproteins.

RNA affinity tags would be very useful for the study of RNAs and ribonucleoproteins (RNPs) as a means for rapid detection, immobilization, and purification. To develop a new affinity tag, streptavidin-binding RNA ligands, termed "aptamers," were identified from a random RNA library using in vitro selection. Individual aptamers were classified into two groups based on common sequences, and representative members of the groups had sufficiently low dissociation constants to suggest they would be useful affinity tools. Binding of the aptamers to streptavidin was blocked by presaturation of the streptavidin with biotin, and biotin could be used to dissociate RNA/streptavidin complexes. To investigate the practicality of using the aptamer as an affinity tag, one of the higher affinity aptamers was inserted into RPR1 RNA, the large RNA subunit of RNase P. The aptamer-tagged RNase P could be specifically isolated using commercially available streptavidin-agarose and recovered in a catalytically active form when biotin was used as an eluting agent under mild conditions. The aptamer tag was also used to demonstrate that RNase P exists in a monomeric form, and is not tightly associated with RNase MRP, a closely related ribonucleoprotein enzyme. These results show that the streptavidin aptamers are potentially powerful tools for the study of RNAs or RNPs.

Sephadex-binding RNA ligands: rapid affinity purification of RNA from complex RNA mixtures.

Sephadex-binding RNA ligands (aptamers) were obtained through in vitro selection. They could be classified into two groups based on their consensus sequences and the aptamers from both groups showed strong binding to Sephadex G-100. One of the highest affinity aptamers, D8, was chosen for further characterization. Aptamer D8 bound to dextran B512, the soluble base material of Sephadex, but not to isomaltose, isomaltotriose and isomaltotetraose, suggesting that its optimal binding site might consist of more than four glucose residues linked via alpha-1,6 linkages. The aptamer was very specific to the Sephadex matrix and did not bind appreciably to other supporting matrices, such as Sepharose, Sephacryl, cellulose or pustulan. Using Sephadex G-100, the aptamer could be purified from a complex mixture of cellular RNA, giving an enrichment of at least 60 000-fold, compared with a non-specific control RNA. These RNA aptamers can be used as affinity tags for RNAs or RNA subunits of ribonucleoproteins to allow rapid purification from complex mixtures of RNA using only Sephadex.

Functional dissection of the dimerization and enzymatic activities of Escherichia coli nitrogen regulator II and their regulation by the PII protein.

The dimeric two-component system transmitter protein NRII (NtrB) of Escherichia coli, product of glnL (ntrB), controls transcription of nitrogen-regulated genes by catalyzing the phosphorylation and dephosphorylation of the transcription factor NRI (NtrC). Previous studies showed that the PII signal transduction protein inhibits the kinase activity of NRII and activates its phosphatase activity. We observed that PII greatly stimulated the NRII phosphatase activity under conditions where the cleavage of ATP was prevented, indicating that the phosphatase activity did not result simply from prevention of the antagonistic NRII kinase activity by PII. Rather, PII was an activator of the phosphatase activity. To study this regulation, we examined the dimerization and enzymatic activities of NRII and various polypeptides derived from NRII, and their regulation by PII. Our results were consistent with the hypothesis that NRII consists of three domains: an N-terminal domain found only in NRII proteins and two domains formed by the conserved transmitter module of NRII, the phosphotransferase/phosphatase/dimerization (central) domain and the kinase domain. All three domains were involved in regulating the kinase and phosphatase activities of NRII. The N-terminal domain was involved in intramolecular signal transduction, and controlled access to the NRII active site for the isolated dimeric central domain added in trans. The central domain was responsible for dimerization and the phosphotransferase and phosphatase activities of NRII, but the latter activity was weak in the isolated domain and was not regulated by PII. The C-terminal kinase domain was responsible for the kinase activity. The PII protein appeared to interact with the isolated transmitter module of NRII, and not with the N-terminal domain as previously thought, since PII dramatically increased the stoichiometry of autophosphorylation of the isolated transmitter module. However, the phosphatase activity of the transmitter module of NRII was low even in the presence of PII, suggesting that the N-terminal domain was necessary for the central domain to assume the conformation necessary for potent phosphatase activity. Also, PII significantly reduced the rate of transphosphorylation of the isolated central domain by the isolated kinase domain, suggesting that PII interacts directly with the kinase domain. We hypothesize that the binding of PII to the kinase domain of NRII results in an altered conformation that is transmitted to the central and N-terminal domains; this causes the central domain to assume the conformation with potent phosphatase activity.

Neonatal screening for congenital hypothyroidism and phenylketonuria at Siriraj Hospital, Mahidol University, Bangkok, Thailand--a pilot study.

A newborn screening program for congenital hypothyroidism (CH) and phenylketonuria (PKU), a pilot study, was initiated at the Medical Genetics Unit, Department of Pediatrics, Siriraj Hospital Faculty of Medicine, Mahidol University in Bangkok, Thailand from January 1994 to December 1998, using dried blood spots (DBS). A total of 18,739 infants (out of 85,150 livebirths) were screened (22 % coverage). Three cases of congenital hypothyroidism (CH) were identified (incidence of 1: 6,246, livebirths), by enzyme linked immunosorbent (ELISA) and fluoroimmunoassays using a cut-off level of TSH >20 microlU/ml: the recall rate of 0.24%. The screening for PKU was done by fluorometric (Guthrie) and enzyme linked immunosorbent (ELISA) methods; using cut-off levels of phenylalanine > 4 mg/dl and > 3.6 mg/dl respectively, with a recall rate of 0.13%. There was no PKU found. Our study, a voluntary program, emphasizes the importance of parental education and consent; specimen collection and handling; appropriate follow-up and referral to specialists for treatment and counseling. Routine newborn screening for CH and PKU is being established to ascertain the maximum coverage, using recommendations and guidelines from this pilot study.

Establishment of OVS1 and OVS2 monoclonal antibodies recognizing human ovarian mucinous cystadenocarcinoma.

Two newly established murine monoclonal antibodies (MAbs), OVS1 and OVS2, to human ovarian mucinous cystadenocarcinoma were further characterized for diagnostic efficacy. The specific SA-1 antigen, purified from the tumor extract was identified as a glycoprotein of 29 kDa. A double determinant biotinstreptavidin alkaline phosphatase immunoassay system, containing OVS1 and OVS2 MAbs was used to determine the SA-1 levels in serum. The OVS1 MAb was used as a first antibody because of its high specificity of 96% while OVS2 MAb, with a lower specificity of 8% but greater sensitivity of 78%, was chosen as a second antibody. Matched sera of 64 healthy controls and 90 patients with definite diagnoses of 25 benign diseases, 14 nonovarian cancer and 51 ovarian cancer, were simultaneously measured together with CA 125 values. At cut-off levels of 220 and 360 units/ml, the SA-1 test showed 63% and 43% positive rates respectively in all types of ovarian cancer, compared to 65% and 57% positive rates for CA 125 at cut-off levels of 35 and 60 units/ml, respectively. Sensitivity for SA-1 at 220 units/ml cut-off level in mucinous ovarian cancer was 75% and increased significantly to 85% when the test was combined with CA 125 at 35 units/ml cut-off level. Furthermore, The combination of both tests significantly increased the positive rates to 86% in all types of early stage ovarian cancer.(ABSTRACT TRUNCATED AT 250 WORDS)