Folding of 16S rRNA in a Signal‐Producing Structure for the Detection of Bacteria

Gerasimova, Yulia V.; Kolpashchikov, Dmitry M.

doi:10.1002/anie.201303919

Cited by 40 publications

(40 citation statements)

References 20 publications

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“…3A). This is consistent with the high selectivity of the BiDz sensors reported earlier (Kolpashchikov 2007(Kolpashchikov , 2010Mokany et al 2010;Gerasimova and Kolpashchikov 2013a;Gerasimova et al 2010Gerasimova et al , 2013.…”

Section: Characterization Of the Bidz Sensorssupporting

confidence: 92%

“…The LOD for the sensors calculated as 3σ/slope was found to be in the range of 2-7 pM. These values are in accordance with the LOD found previously for other BiDz sensors (Gerasimova and Kolpashchikov 2013a;Gerasimova et al 2010Gerasimova et al , 2013. The linear slope for BiDz0 was greater than that for BiDz-m04 (the slope ratio was 4.38).…”

Section: Characterization Of the Bidz Sensorssupporting

confidence: 89%

“…The new technique takes advantage of recent developments in the field of functional DNA biochemistry, namely, binary deoxyribozyme sensors (Kolpashchikov 2007(Kolpashchikov , 2010Mokany et al 2010;Gerasimova and Kolpashchikov 2013a;Gerasimova et al 2010Gerasimova et al , 2013. The BiDz sensors developed in this work recognize the targeted rRNA sequence with high selectivity and a detection limit of ∼2-7 pM.…”

Section: Discussionmentioning

confidence: 99%

“…Binary probes demonstrate excellent selectivity, being capable of differentiating even single-base substitutions in DNA and RNA analytes (Kolpashchikov 2010). Here, we used binary deoxyribozyme (BiDz) sensors based on split 10-23 deoxyribozyme introduced originally by Mokany et al (2010) and used by us recently for detection of E. coli cells (Gerasimova and Kolpashchikov 2013a) and analysis of Mycobacterium tuberculosis RNA (Gerasimova et al 2013). The sequences of Dz a , Dz b , and the reporter substrate used in this study are listed in Table 1.…”

Section: Design Of Binary Deoxyribozyme (Bidz) Sensorsmentioning

confidence: 99%

“…Deoxyribozymes (Dz) are artificial catalytic DNA molecules (Emilsson and Breaker 2002) that are used as sensors for metal ions (Lan and Lu 2012), proteins (Stojanovic et al 2000), small biological molecules (Liu et al 2009), and nucleic acids (Stojanovic et al 2001;Kolpashchikov 2007Kolpashchikov , 2010Mokany et al 2010;Gerasimova and Kolpashchikov 2013a;Gerasimova et al 2010Gerasimova et al , 2013Sando et al 2013;Zagorovsky and Chan 2013). Here, we take advantage of binary deoxyribozyme (BiDz) fluorescent sensors (Kolpashchikov 2007;Gerasimova et al 2010;Mokany et al 2010) to replace the tedious primer extension assay for E. coli rRNA analysis.…”

Section: Introductionmentioning

confidence: 99%

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Expedited quantification of mutant ribosomal RNA by binary deoxyribozyme (BiDz) sensors

Gerasimova

Yakovchuk

Dedkova

et al. 2015

RNA

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Mutations in ribosomal RNA (rRNA) have traditionally been detected by the primer extension assay, which is a tedious and multistage procedure. Here, we describe a simple and straightforward fluorescence assay based on binary deoxyribozyme (BiDz) sensors. The assay uses two short DNA oligonucleotides that hybridize specifically to adjacent fragments of rRNA, one of which contains a mutation site. This hybridization results in the formation of a deoxyribozyme catalytic core that produces the fluorescent signal and amplifies it due to multiple rounds of catalytic action. This assay enables us to expedite semiquantification of mutant rRNA content in cell cultures starting from whole cells, which provides information useful for optimization of culture preparation prior to ribosome isolation. The method requires less than a microliter of a standard Escherichia coli cell culture and decreases analysis time from several days (for primer extension assay) to 1.5 h with hands-on time of ∼10 min. It is sensitive to single-nucleotide mutations. The new assay simplifies the preliminary analysis of RNA samples and cells in molecular biology and cloning experiments and is promising in other applications where fast detection/ quantification of specific RNA is required.

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