Turn-on RNA Mango Beacons for trans-acting fluorogenic nucleic acid detection

The Mango I and II RNA aptamers have been widely used in vivo and in vitro as genetically encodable fluorogenic markers that undergo large increases in fluorescence upon binding to their ligand, TO1-Biotin. However, while studying nucleic acid sequences, it is often desirable to have trans-acting probes that induce fluorescence upon binding to a target sequence. Here, we rationally design three types of light-up RNA Mango Beacons based on a minimized Mango core that induces fluorescence upon binding to a target RNA strand. Our first design is bimolecular in nature and uses a DNA inhibition strand to prevent folding of the Mango aptamer core until binding to a target RNA. Our second design is unimolecular in nature, and features hybridization arms flanking the core that inhibit G-quadruplex folding until refolding is triggered by binding to a target RNA strand. Our third design builds upon this structure, and incorporates a self-inhibiting domain into one of the flanking arms that deliberately binds to, and precludes folding of, the aptamer core until a target is bound. This design separates G-quadruplex folding inhibition and RNA target hybridization into separate modules, enabling a more universal unimolecular beacon design. All three Mango Beacons feature high contrasts and low costs when compared to conventional molecular beacons, with excellent potential for in vitro and in vivo applications.

Monitoring stability indicating impurities and aldehyde content in lipid nanoparticle raw material and formulated drugs

Lipid nanoparticles (LNPs) are designed to protect and transport sensitive payloads or active pharmaceutical ingredients as part of new therapeutic modalities. As a multi-component particle, a high degree of quality control is necessary to ensure raw materials are free of critical impurities that could adversely impact the drug product. In this study, we demonstrate a reversed phase liquid chromatography method hyphenated with a single quadrupole mass spectrometer (RPLC-MS) as an alternative platform to methods that incorporate evaporative light scattering or charged aerosol detectors in the detection and quantitation of critical impurities associated with LNPs. The proposed RPLC-MS method offers an increase of up to 2 orders of magnitude in dynamic range and 3 orders of magnitude in sensitivity in the analysis of impurities associated with LNPs compared to conventional detectors. Access to complementary mass data enabled the detection and identification of stability indicating impurities as part of stress studies carried out on an ionizable lipid. In addition to confirmation of peak identity, complementary mass data was also used to assess residual aldehydes in raw material and formulated LNPs in accordance with regulatory guidance. Following derivatization using 2,4-dinitrophenylhydrazine, aldehyde content in the ionizable lipid raw material was determined to exceed the reporting threshold of 0.05% in 30% of the test cases. The experimental findings observed in this study demonstrate the utility of the proposed RPLC-MS method in the identification and monitoring of stability-indicating attributes associated with LNPs as part of current Good Manufacturing Practices for improved consumer safety in drug products.

Processive RNA polymerization and promoter recognition in an RNA World

Early life is thought to have required the self-replication of RNA by RNA replicases. However, how such replicases evolved and subsequently enabled gene expression remains largely unexplored. We engineered and selected a holopolymerase ribozyme that uses a sigma factor-like specificity primer to first recognize an RNA promoter sequence and then, in a second step, rearrange to a processive elongation form. Using its own sequence, the polymerase can also program itself to polymerize from certain RNA promoters and not others. This selective promoter-based polymerization could allow an RNA replicase ribozyme to define "self" from "nonself," an important development for the avoidance of replicative parasites. Moreover, the clamp-like mechanism of this polymerase could eventually enable strand invasion, a critical requirement for replication in the early evolution of life.

Microchip RT-PCR Detection of Nasopharyngeal SARS-CoV-2 Samples

Fast, accurate, and reliable diagnostic tests are critical for controlling the spread of the coronavirus disease 2019 (COVID-19) associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The current gold standard for testing is real-time PCR; however, during the current pandemic, supplies of testing kits and reagents have been limited. We report the validation of a rapid (30 minutes), user-friendly, and accurate microchip real-time PCR assay for detection of SARS-CoV-2 from nasopharyngeal swab RNA extracts. Microchips preloaded with COVID-19 primers and probes for the N gene accommodate 1.2-μL reaction volumes, lowering the required reagents by 10-fold compared with tube-based real-time PCR. We validated our assay using contrived reference samples and 21 clinical samples from patients in Canada, determining a limit of detection of 1 copy per reaction. The microchip real-time PCR provides a significantly lower resource alternative to the Centers for Disease Control and Prevention–approved real-time RT-PCR assays with comparable sensitivity, showing 100% positive and negative predictive agreement of clinical samples.

Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair

Fluorescent RNA aptamers have been used in cells as biosensor reporters and tags for tracking transcripts. Recently, combined SELEX and microfluidic fluorescence sorting yielded three aptamers that activate fluorescence of TO1-Biotin: Mango-II, Mango-III, and Mango-IV. Of these, Mango-IV was best at imaging RNAs in both fixed and live mammalian cells. To understand how Mango-IV achieves activity in cells, we determined its crystal structure complexed with TO1-Biotin. The structure reveals a domain-swapped homodimer with two independent G-quadruplex fluorophore binding pockets. Structure-based analyses indicate that the Mango-IV core has relaxed fluorophore specificity, and a tendency to reorganize binding pocket residues. These molecular properties may endow it with robustness in the cellular milieu. Based on the domain-swapped structure, heterodimers between Mango-IV and the fluorescent aptamer iSpinach, joined by Watson-Crick base pairing, were constructed. These exhibited FRET between their respective aptamer-activated fluorophores, advancing fluorescent aptamer technology toward multi-color, RNA-based imaging of RNA coexpression and colocalization.

Structure and functional reselection of the Mango-III fluorogenic RNA aptamer

Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A10U), and a functionally reselected mutant iMango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range trans Watson-Crick pair (whose A10U mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved iMango-III and Mango-III(A10U) fluoresce ~50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization.

Crystal Structures of the Mango-II RNA Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness

Several RNA aptamers that bind small molecules and enhance their fluorescence have been successfully used to tag and track RNAs in vivo, but these genetically encodable tags have not yet achieved single-fluorophore resolution. Recently, Mango-II, an RNA that binds TO1-Biotin with ∼1 nM affinity and enhances its fluorescence by >1500-fold, was isolated by fluorescence selection from the pool that yielded the original RNA Mango. We determined the crystal structures of Mango-II in complex with two fluorophores, TO1-Biotin and TO3-Biotin, and found that despite their high affinity, the ligands adopt multiple distinct conformations, indicative of a binding pocket with modest stereoselectivity. Mutational analysis of the binding site led to Mango-II(A22U), which retains high affinity for TO1-Biotin but now discriminates >5-fold against TO3-biotin. Moreover, fluorescence enhancement of TO1-Biotin increases by 18%, while that of TO3-Biotin decreases by 25%. Crystallographic, spectroscopic, and analogue studies show that the A22U mutation improves conformational homogeneity and shape complementarity of the fluorophore-RNA interface. Our work demonstrates that even after extensive functional selection, aptamer RNAs can be further improved through structure-guided engineering.

Transitioning to DNA genomes in an RNA world

The unexpected ability of an RNA polymerase ribozyme to copy RNA into DNA has ramifications for understanding how DNA genomes evolved.

RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking

Because RNA lacks strong intrinsic fluorescence, it has proven challenging to track RNA molecules in real time. To address this problem and to allow the purification of fluorescently tagged RNA complexes, we have selected a high affinity RNA aptamer called RNA Mango. This aptamer binds a series of thiazole orange (fluorophore) derivatives with nanomolar affinity, while increasing fluorophore fluorescence by up to 1,100-fold. Visualization of RNA Mango by single-molecule fluorescence microscopy, together with injection and imaging of RNA Mango/fluorophore complex in C. elegans gonads demonstrates the potential for live-cell RNA imaging with this system. By inserting RNA Mango into a stem loop of the bacterial 6S RNA and biotinylating the fluorophore, we demonstrate that the aptamer can be used to simultaneously fluorescently label and purify biologically important RNAs. The high affinity and fluorescent properties of RNA Mango are therefore expected to simplify the study of RNA complexes.

Molecular characterization of Mycobacterium bovis BCG: Romanian sub-strain

The Romanian sub-strain used for BCG vaccine production was characterized by polymorphic GC-rich repetitive sequence (PGRS) restriction profile and IS6110 detection. For comparison, the Pasteur and Moscow Mycobacterium bovis BCG sub-strains, M. bovis AN5, and M. tuberculosis H37Rv were analyzed. The BCG sub-strains showed the same restriction profile for PGRS after Pvu II, BamH I and Sal I digestion. They could be distinguished from the strains M. bovis AN5 and M. tuberculosis H37Rv after Pvu II and Sal I digestion. Sal I can also distinguish between M. bovis AN5 and M. tuberculosis H37Rv. Digestion with Pvu II, Sal I, Sca I, Mlu I and BamH I gave identical profiles of IS6110 hybridization for the Romanian and Pasteur BCG substrains.

[The clinico-epidemiological characteristics of HIV infection in 93 adults in the Republic of Moldova]

We have examined 93 adults HIV serum-positive (citizens of Moldova Republic), admitted in 1994-1998 (months I-VIII) to the Hospital of Infections Diseases 'T. Ciorba'--Kishinev. Since 1996 the number of HIV infected people began to grow up rapidly. Most affected group was those of 16-29 years old people--78.4%. The major way of the HIV transmission was the use of intravenous drugs (81.7%). Number of men i.v. drug users was two time greater then women's (88.9%/66.7%). At the time of HIV infection diagnosis 77.9% of patients were in the clinical category A, 16.9% in B and 5.2% in C (1993 classification system, CDC-Atlanta). During the control period seven persons were redistributed from the clinical category A to B and two from A to C. A high prevalence value for tuberculosis in AIDS (71.4%) has been observed, this infection being the first manifestation of stadium C in 57.1% of cases. The circulation of hepatitis viruses is high in the drug users community: the markers of VHC were detected in 84.2%, HBsAg in 17.1% and VHD antibodies in 9.2%.

[The clinico-epidemiological aspects of HIV infection in 167 children nonmaternally infected who have died with a diagnosis of AIDS]

The aim of this study was to evaluate the clinical and epidemiological particularity of pediatrics nosocomial HIV infection. Our study group consists of 167 HIV serum-positive nonmaternally infected children who died of AIDS in 1990-1997 (inclusive) in Colentina Hospital of Infections Diseases--Bucharest. Fifty per cent of institutionalized children and 28% of family children died in the first two years of life. About 80% of children were revealed too late as HIV infected. It has been observed a relatively high prevalence values for: multiple or recurrent pneumonia--74.8%, recurrent or chronic diarrhea--87.4%, encephalopathy--65.8%, weight-growth deficiency--100%, disseminated or extrapulmonary tuberculosis--13.8%, HBsAg carriage--59.8%; and low prevalence values for: lymphoid interstitial pneumonia--16.5%, Pneumocystis carinii pneumonia--11.4%, cytomegalovirus diseases--1.8%, cryptosporidiosis--1.8%. The evolution of HIV infection (weight-growth deficiency and encephalopathy) were aggravated in hospitalised children (especially, in the first two years of life). Nutrition and hygiene care factors positively influence the evolution of HIV infection. Multiple or recurrent pneumonia are out of an important prognostic value in the appreciation of SIDA evolution. The incidence and severity of tuberculosis increased at older children. The too late diagnostic of HIV infection had unfavourable influence upon the life expectancy of children.

[The action of HIV infection on the height-weight development of children infected postnatally]

The purpose of the recent research was to evaluate the influence of HIV infection on the weight-growth deficiency of nonmaternally infected children. The retrospective and prospective study was done on 141 children who died of AIDS in 1990-1997 (inclusive) in Colentina Hospital of Infectious Diseases, Bucharest. The mean of weight and growth deficiency in the total group was accordingly 50.7% and 20.4% with a statistically significant differences in organized children 54.3% and 21.3% in comparison with those of family 46.4% and 18.5%. The evaluation of the anthropometry data estimates a relationship of middle strength between weight and growth deficiency. The obtained data reveal the importance of nutrition and hygiene care factors in the degree of wasting syndrome and mortality-rate, especially in the first two years of life, and demonstrate the necessity of anthropometry measures of children in AIDS.