Screening oligonucleotide sequences for silver staining and d-galactose visual detection using RCA silver staining in a tube

Chen, Ziwei; Duan, Xuying; Hua, Wei; Tang, Suming; Xu, Chen; Li, Yanlei; Guan, Yifu; Zhao, Guojie

doi:10.1093/abbs/gmy034

Cited by 3 publications

(1 citation statement)

References 40 publications

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“…The nucleotide contents of circular templates have been found to affect RCA efficiency [12] . The nucleotide types of templates affect visualization detection of RCA by silver staining [13] . The template lengths are related to a sinuous phenomenon of RCA efficiency [14] .…”

Section: Introductionmentioning

confidence: 99%

Revealing an initiation inhibition of RCA and its application in nucleic acid detection

Zhang¹,

Ge²,

Yu³

et al. 2023

ABBS

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Rolling circle amplification is a widely used biosensing technique. Although various secondary structures have been employed in RCA, their effects on RCA efficiency have seldom been reported. Here, we find that stems in circular templates can strongly inhibit RCA, and the primer-stem distance is responsible for the inhibition. Based on the results, we propose an initiation inhibition mechanism and present a design principle for a general RCA assay. Inspired by this mechanism, we further propose a new nucleic acid detection method. The results verify that this method can increase RCA detection sensitivity according to the target recycling principle. Besides DNA detection, it can also achieve single mismatch discrimination of miRNA detection after optimization. This method also shows convenient visualization detection. The initiation inhibition of RCA could be helpful for RCA applications as promising detection techniques.

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Section: Introductionmentioning

confidence: 99%

Revealing an initiation inhibition of RCA and its application in nucleic acid detection

Zhang¹,

Ge²,

Yu³

et al. 2023

ABBS

Self Cite

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Influence of Nucleotide-biased Fluorescence Emissions of SYBR Green II on the Result Consistence of Rolling Circle Amplification

Zhang¹,

Jiang²,

Yuan³

et al. 2019

Chem. Res. Chin. Univ.

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Screening substrate-binding positions by rolling circle amplification suggesting a binding model of Nt.BstNBI

Hua

Tang

Duan

et al. 2019

Biochemical Journal

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Nicking endonucleases (NEs) become increasingly attractive for their promising applications in isothermal amplification. Unfortunately, in comparison with their applications, their catalytic mechanism studies have relatively lagged behind due to a paucity of crystal structure information. Nt.BstNBI is one of those widely used NEs. However, many aspects of its catalytic mechanism still remained to be explored. Herein, we employed only rolling circle amplification (RCA) assay as a major analytic tool and succeeded in identifying the potential binding positions and regions of the DNA substrate based on locked nucleic acid modification, DNA duplex length of substrate, and substrate mismatch designs. Based on these data, we, for the first time, revealed that Nt.BstNBI was likely to recognize six adjacent positions of the recognition sequence (G1rt, A2rt, G3rt, A2rb, C3rb, and T4rb) in the major groove and hold three positions of the cleavage sequence (N3ct, N4ct, and N7cb) in the minor groove of DNA duplex for nicking. Moreover, this work also demonstrated the unexpected efficiency of RCA to study the macromolecular interaction for certain kind of nucleases in an easy and high-throughput way.

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Screening oligonucleotide sequences for silver staining and d-galactose visual detection using RCA silver staining in a tube

Cited by 3 publications

References 40 publications

Revealing an initiation inhibition of RCA and its application in nucleic acid detection

Revealing an initiation inhibition of RCA and its application in nucleic acid detection

Influence of Nucleotide-biased Fluorescence Emissions of SYBR Green II on the Result Consistence of Rolling Circle Amplification

Screening substrate-binding positions by rolling circle amplification suggesting a binding model of Nt.BstNBI

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