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  1. Article ; Online: Computational design and experimental verification of pseudoknotted ribozymes.

    Najeh, Sabrine / Zandi, Kasra / Kharma, Nawwaf / Perreault, Jonathan

    RNA (New York, N.Y.)

    2023  Volume 29, Issue 6, Page(s) 764–776

    Abstract: The design of new RNA sequences that retain the function of a model RNA structure is a challenge in bioinformatics because of the structural complexity of these molecules. RNA can fold into its secondary and tertiary structures by forming stem-loops and ... ...

    Abstract The design of new RNA sequences that retain the function of a model RNA structure is a challenge in bioinformatics because of the structural complexity of these molecules. RNA can fold into its secondary and tertiary structures by forming stem-loops and pseudoknots. A pseudoknot is a set of base pairs between a region within a stem-loop and nucleotides outside of this stem-loop; this motif is very important for numerous functional structures. It is important for any computational design algorithm to take into account these interactions to give a reliable result for any structures that include pseudoknots. In our study, we experimentally validated synthetic ribozymes designed by Enzymer, which implements algorithms allowing for the design of pseudoknots. Enzymer is a program that uses an inverse folding approach to design pseudoknotted RNAs; we used it in this study to design two types of ribozymes. The ribozymes tested were the hammerhead and the
    MeSH term(s) RNA, Catalytic/chemistry ; RNA/genetics ; RNA/chemistry ; Base Pairing ; Algorithms ; Nucleotides ; Nucleic Acid Conformation
    Chemical Substances RNA, Catalytic ; RNA (63231-63-0) ; Nucleotides
    Language English
    Publishing date 2023-03-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.079148.122
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  2. Article ; Online: Small RNAs beyond Model Organisms: Have We Only Scratched the Surface?

    Boutet, Emilie / Djerroud, Samia / Perreault, Jonathan

    International journal of molecular sciences

    2022  Volume 23, Issue 8

    Abstract: Small RNAs (sRNAs) are essential regulators in the adaptation of bacteria to environmental changes and act by binding targeted mRNAs through base complementarity. Approximately 550 distinct families of sRNAs have been identified since their initial ... ...

    Abstract Small RNAs (sRNAs) are essential regulators in the adaptation of bacteria to environmental changes and act by binding targeted mRNAs through base complementarity. Approximately 550 distinct families of sRNAs have been identified since their initial characterization in the 1980s, accelerated by the emergence of RNA-sequencing. Small RNAs are found in a wide range of bacterial phyla, but they are more prominent in highly researched model organisms compared to the rest of the sequenced bacteria. Indeed,
    MeSH term(s) Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial ; RNA, Bacterial/metabolism ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/metabolism ; Salmonella enterica/genetics ; Salmonella enterica/metabolism ; Sequence Analysis, RNA
    Chemical Substances RNA, Bacterial ; RNA, Small Untranslated
    Language English
    Publishing date 2022-04-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23084448
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  3. Article ; Online: Electrochemically Exfoliated Graphene Oxide for Simple Fabrication of Cocaine Aptasensors.

    Lei, Yuting / Ossonon, Benjamin D / Trahan, Pierre-Luc / Chen, Jiyun / Perreault, Jonathan / Tavares, Ana C

    ACS applied materials & interfaces

    2023  Volume 15, Issue 29, Page(s) 35580–35589

    Abstract: Transducers made from graphene-type materials are widely used in sensing applications. However, utilization of graphene oxide obtained from electrochemical exfoliation of graphite (EGO) has remained relatively unexplored. In this study, electrochemical ... ...

    Abstract Transducers made from graphene-type materials are widely used in sensing applications. However, utilization of graphene oxide obtained from electrochemical exfoliation of graphite (EGO) has remained relatively unexplored. In this study, electrochemical cocaine aptasensors based on large-size EGO flakes were investigated. In particular, the influence of the following parameters on the sensor performance was examined: (i) aptamer's terminal group (-NH
    Language English
    Publishing date 2023-07-13
    Publishing country United States
    Document type Journal Article
    ISSN 1944-8252
    ISSN (online) 1944-8252
    DOI 10.1021/acsami.3c03777
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  4. Article ; Online: Simple rolling circle amplification colorimetric assay based on pH for target DNA detection.

    Hamidi, Seyed Vahid / Perreault, Jonathan

    Talanta

    2019  Volume 201, Page(s) 419–425

    Abstract: Detection and identification of DNA by PCR has opened tremendous possibilities and allows detection of minute quantities of DNA highly specifically. However, PCR remains confined to laboratory settings because of the need of thermocyclers and other ... ...

    Abstract Detection and identification of DNA by PCR has opened tremendous possibilities and allows detection of minute quantities of DNA highly specifically. However, PCR remains confined to laboratory settings because of the need of thermocyclers and other analytical equipment. This led to development of isothermal amplification techniques, among which Pad Lock Probe (PLP)-based Rolling Circle Amplification (RCA) has several advantages, but typically also requires a laboratory apparatus of some sort to measure DNA amplification. To circumvent this limitation, while still taking advantage of PLP-based RCA, we developed a colorimetric assay that relies on pH change. Using this assay, we can detect DNA in the low picomolar range and obtain results observable with the naked eye in only 20 min without any requirement for a thermocycler or other complex device, making it a particularly portable assay.
    MeSH term(s) Animals ; Bacteriophage M13/genetics ; Biosensing Techniques/methods ; Calibration ; Colorimetry/methods ; DNA, Viral/blood ; DNA, Viral/genetics ; DNA-Directed DNA Polymerase/genetics ; Hydrogen-Ion Concentration ; Indicators and Reagents/chemistry ; Influenza A Virus, H5N1 Subtype/genetics ; Limit of Detection ; Nucleic Acid Amplification Techniques/methods ; Nucleic Acid Hybridization ; Phenolsulfonphthalein/chemistry ; Polymorphism, Single Nucleotide ; Rats
    Chemical Substances DNA, Viral ; Indicators and Reagents ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; Phenolsulfonphthalein (I6G9Y0J1OJ)
    Language English
    Publishing date 2019-04-05
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1500969-5
    ISSN 1873-3573 ; 0039-9140
    ISSN (online) 1873-3573
    ISSN 0039-9140
    DOI 10.1016/j.talanta.2019.04.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Fluoride-Controlled Riboswitch-Based Dampening of Gene Expression for Cloning Potent Promoters.

    Korniakova, Vesta / Devinck, Aurélie / Groleau, Marie-Christine / Déziel, Eric / Perreault, Jonathan

    Frontiers in genetics

    2022  Volume 12, Page(s) 591543

    Abstract: Bioreporter systems based on detectable enzyme activity, such as that of beta-galactosidase or luciferase, are key in novel bacterial promoter discovery and study. While these systems permit quantification of gene expression, their use is limited by the ... ...

    Abstract Bioreporter systems based on detectable enzyme activity, such as that of beta-galactosidase or luciferase, are key in novel bacterial promoter discovery and study. While these systems permit quantification of gene expression, their use is limited by the toxicity of the expressed reporter enzymes in a given host. Indeed, the most potent promoters may be overlooked if their activity causes a lethal overproduction of the reporter genes when screening for transcriptional activity of potential promoter sequences with the
    Language English
    Publishing date 2022-01-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2021.591543
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  6. Article ; Online: Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.

    Najeh, Sabrine / Zandi, Kasra / Djerroud, Samia / Kharma, Nawwaf / Perreault, Jonathan

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2167, Page(s) 91–111

    Abstract: Pseudoknots are important motifs for stabilizing the structure of functional RNAs. As an example, pseudoknotted hammerhead ribozymes are highly active compared to minimal ribozymes. The design of new RNA sequences that retain the function of a model RNA ... ...

    Abstract Pseudoknots are important motifs for stabilizing the structure of functional RNAs. As an example, pseudoknotted hammerhead ribozymes are highly active compared to minimal ribozymes. The design of new RNA sequences that retain the function of a model RNA structure includes taking in account pseudoknots presence in the structure, which is usually a challenge for bioinformatics tools. Our method includes using "Enzymer," a software for designing RNA sequences with desired secondary structures that may include pseudoknots. Enzymer implements an efficient stochastic search and optimization algorithm to sample RNA sequences from low ensemble defect mutational landscape of an initial design template to generate an RNA sequence that is predicted to fold into the desired target structure.
    MeSH term(s) Algorithms ; Base Sequence ; Computational Biology/methods ; Computer-Aided Design ; Electrophoresis, Agar Gel ; Electrophoresis, Polyacrylamide Gel ; In Vitro Techniques ; Kinetics ; Nucleic Acid Conformation ; Nucleotide Motifs/genetics ; Polymerase Chain Reaction/methods ; RNA/genetics ; RNA Folding/genetics ; RNA, Catalytic/chemistry ; RNA, Catalytic/genetics ; RNA, Catalytic/metabolism ; Software ; Synthetic Biology/methods ; Transcription, Genetic
    Chemical Substances RNA, Catalytic ; hammerhead ribozyme ; RNA (63231-63-0)
    Language English
    Publishing date 2020-07-24
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0716-9_7
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  7. Article ; Online: Digital Microfluidics Chips for the Execution and Real-Time Monitoring of Multiple Ribozymatic Cleavage Reactions.

    Davis, Alen N / Samlali, Kenza / Kapadia, Jay B / Perreault, Jonathan / Shih, Steve C C / Kharma, Nawwaf

    ACS omega

    2021  Volume 6, Issue 35, Page(s) 22514–22524

    Abstract: In this paper, we describe the design and performance of two digital microfluidics (DMF) chips capable of executing multiple ribozymatic reactions, with proper controls, in response to short single-stranded DNA inducers. Since the fluorescence output of ... ...

    Abstract In this paper, we describe the design and performance of two digital microfluidics (DMF) chips capable of executing multiple ribozymatic reactions, with proper controls, in response to short single-stranded DNA inducers. Since the fluorescence output of a reaction is measurable directly from the chip, without the need for gel electrophoresis, a complete experiment involving up to eight reactions (per chip) can be carried out reliably, relatively quickly, and efficiently. The ribozymes can also be used as biosensors of the concentration of oligonucleotide inputs, with high sensitivity, low limits of quantification and of detection, and excellent signal-to-noise ratio. The presented chips are readily usable devices that can be used to automate, speed up, and reduce the costs of ribozymatic reaction experiments.
    Language English
    Publishing date 2021-08-25
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.1c00239
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  8. Article ; Online: Toehold-mediated strand displacement to measure released product from self-cleaving ribozymes.

    Kapadia, Jay Bhakti / Kharma, Nawwaf / Davis, Alen Nellikulam / Kamel, Nicolas / Perreault, Jonathan

    RNA (New York, N.Y.)

    2021  Volume 28, Issue 2, Page(s) 263–273

    Abstract: This paper presents a probe comprising a fluorophore and a quencher, enabling measurement of released product from self-cleaving hammerhead ribozyme, without labeled RNA molecules, regular sampling or use of polyacrylamide gels. The probe is made of two ... ...

    Abstract This paper presents a probe comprising a fluorophore and a quencher, enabling measurement of released product from self-cleaving hammerhead ribozyme, without labeled RNA molecules, regular sampling or use of polyacrylamide gels. The probe is made of two DNA strands; one strand is labeled with a fluorophore at its 5'-end, while the other strand is labeled with a quencher at its 3'-end. These two DNA strands are perfectly complementary, but with a 3'-overhang of the fluorophore strand. These unpaired nucleotides act as a toehold, which is utilized by a detached cleaved fragment (coming from a self-cleaving hammerhead ribozyme) as the starting point for a strand displacement reaction. This reaction causes the separation of the fluorophore strand from the quencher strand, culminating in fluorescence, detectable in a plate reader. Notably, the emitted fluorescence is
    MeSH term(s) DNA/chemistry ; Fluorescent Dyes/chemistry ; RNA/chemistry ; RNA, Catalytic/chemistry ; RNA, Catalytic/metabolism ; Synthetic Biology
    Chemical Substances Fluorescent Dyes ; RNA, Catalytic ; RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2021-12-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.078823.121
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Single Mutation in Hammerhead Ribozyme Favors Cleavage Activity with Manganese over Magnesium.

    Naghdi, Mohammad Reza / Boutet, Emilie / Mucha, Clarisse / Ouellet, Jonathan / Perreault, Jonathan

    Non-coding RNA

    2020  Volume 6, Issue 1

    Abstract: Hammerhead ribozymes are one of the most studied classes of ribozymes so far, from both the structural and biochemical point of views. The activity of most hammerhead ribozymes is cation-dependent. ... ...

    Abstract Hammerhead ribozymes are one of the most studied classes of ribozymes so far, from both the structural and biochemical point of views. The activity of most hammerhead ribozymes is cation-dependent. Mg
    Language English
    Publishing date 2020-03-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2813993-8
    ISSN 2311-553X ; 2311-553X
    ISSN (online) 2311-553X
    ISSN 2311-553X
    DOI 10.3390/ncrna6010014
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  10. Article ; Online: High-sensitivity small-molecule detection of microcystin-LR cyano-toxin using a terahertz-aptamer biosensor.

    Mohamed, Ahmed / Walsh, Ryan / Cherif, Mohamed / Hafez, Hassan A / Ropagnol, Xavier / Vidal, François / Perreault, Jonathan / Ozaki, Tsuneyuki

    The Analyst

    2021  Volume 146, Issue 24, Page(s) 7583–7592

    Abstract: We demonstrate the rapid and highly sensitive detection of a small molecule, microcystin-LR (MC-LR) toxin using an aptasensor based on a terahertz (THz) emission technique named the terahertz chemical microscope (TCM). The main component of the TCM is ... ...

    Abstract We demonstrate the rapid and highly sensitive detection of a small molecule, microcystin-LR (MC-LR) toxin using an aptasensor based on a terahertz (THz) emission technique named the terahertz chemical microscope (TCM). The main component of the TCM is the sensing plate, which consists of a thin silicon layer deposited on a sapphire substrate, with a natural SiO
    MeSH term(s) Biosensing Techniques ; Limit of Detection ; Marine Toxins ; Microcystins ; Silicon Dioxide
    Chemical Substances Marine Toxins ; Microcystins ; Silicon Dioxide (7631-86-9) ; cyanoginosin LR (EQ8332842Y)
    Language English
    Publishing date 2021-12-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 210747-8
    ISSN 1364-5528 ; 0003-2654
    ISSN (online) 1364-5528
    ISSN 0003-2654
    DOI 10.1039/d1an01577j
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