Characteristics and application of S1–P1 nucleases in biotechnology and medicine

Kovaĺ, T.; Dohnálek, Jan

doi:10.1016/j.biotechadv.2017.12.007

Cited by 18 publications

(14 citation statements)

References 134 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The Chit62J4 adaptation happened away from the actual catalytic site. Similar shifts of pH optima, realized by the overall protein composition rather than active site changes, were seen also in other enzymatic systems, e.g., in non-specific nucleases [ 48 ].…”

Section: Discussionsupporting

confidence: 63%

Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4

et al. 2021

Self Cite

View full text Add to dashboard Cite

Commensal bacterium Clostridium paraputrificum J4 produces several extracellular chitinolytic enzymes including a 62 kDa chitinase Chit62J4 active toward 4-nitrophenyl N,N′-diacetyl-β-d-chitobioside (pNGG). We characterized the crude enzyme from bacterial culture fluid, recombinant enzyme rChit62J4, and its catalytic domain rChit62J4cat. This major chitinase, securing nutrition of the bacterium in the human intestinal tract when supplied with chitin, has a pH optimum of 5.5 and processes pNGG with Km = 0.24 mM and kcat = 30.0 s−1. Sequence comparison of the amino acid sequence of Chit62J4, determined during bacterial genome sequencing, characterizes the enzyme as a family 18 glycosyl hydrolase with a four-domain structure. The catalytic domain has the typical TIM barrel structure and the accessory domains—2x Fn3/Big3 and a carbohydrate binding module—that likely supports enzyme activity on chitin fibers. The catalytic domain is highly homologous to a single-domain chitinase of Bacillus cereus NCTU2. However, the catalytic profiles significantly differ between the two enzymes despite almost identical catalytic sites. The shift of pI and pH optimum of the commensal enzyme toward acidic values compared to the soil bacterium is the likely environmental adaptation that provides C. paraputrificum J4 a competitive advantage over other commensal bacteria.

show abstract

Section: Discussionsupporting

confidence: 63%

Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…In contrast, the C‐clamps largely maintained structural integrity after being processed by the trans‐activated LbCas12a (hereon referred to as Cas12a) and P1 nucleases (Figures S4–S8). The structural damages caused by the S1 and mung bean nucleases are consistent with their reported weak activities of dsDNA digestion, and may be exacerbated by the acidic conditions optimal for their performance . We then tested selected nucleases with the 6 and 12 pN versions of the force clamp.…”

Section: Figurementioning

confidence: 55%

“…Towards this goal, we searched for ssDNA‐specific nucleases that function under the ionic and thermal conditions necessary for the stability of DNA‐origami structures. We considered known endonucleases from the S1‐P1 family, including P1, S1 and mung bean nucleases, as well as the CRISPR‐Cas12a (Cpf1), which can be activated by its sequence‐specific double‐stranded DNA (dsDNA) target (ssDNA activators are less efficient) for nonspecific ssDNA trans‐cleavage . To evaluate the nucleases’ DNA‐origami post‐processing capabilities, we adapted the “force clamp” structure designed by the Liedl group .…”

Section: Figurementioning

confidence: 99%

“…The structural damages caused by the S1 and mung bean nucleases are consistent with their reported weak activities of dsDNA digestion, and may be exacerbated by the acidic conditions optimal for their performance. [5] We then tested selected nucleases with the 6 and 12 pN versions of the force clamp. With slower kinetics, Cas12a cut these ssDNA segments without significantly deforming the clamps (Figure 1 c and S9-S16).…”

mentioning

confidence: 99%

See 1 more Smart Citation

DNA Origami Post‐Processing by CRISPR‐Cas12a

et al. 2020

View full text Add to dashboard Cite

Customizable nanostructures built through the DNA‐origami technique hold tremendous promise in nanomaterial fabrication and biotechnology. Despite the cutting‐edge tools for DNA‐origami design and preparation, it remains challenging to separate structural components of an architecture built from—thus held together by—a continuous scaffold strand, which in turn limits the modularity and function of the DNA‐origami devices. To address this challenge, here we present an enzymatic method to clean up and reconfigure DNA‐origami structures. We target single‐stranded (ss) regions of DNA‐origami structures and remove them with CRISPR‐Cas12a, a hyper‐active ssDNA endonuclease without sequence specificity. We demonstrate the utility of this facile, selective post‐processing method on DNA structures with various geometrical and mechanical properties, realizing intricate structures and structural transformations that were previously difficult to engineer. Given the biocompatibility of Cas12a‐like enzymes, this versatile tool may be programmed in the future to operate functional nanodevices in cells.

show abstract

“…It was first isolated from Aspergillus oryzae by Vogt in 1973 [135]. The primary function of S1 nuclease is to degrade ssDNA or RNA, but its activity is not vigorous when double-stranded substances such as dsDNA and double-stranded RNA are used as substrates [135][136][137]. Therefore, the S1 nuclease is often used as a mediator in FNA biosensors to take advantage of the unique single strand degradation characteristics [59,138,139].…”

Section: S1 Nuclease Based Strategies In Enzyme Mediatorsmentioning

confidence: 99%

Recent Advances on Functional Nucleic-Acid Biosensors

Zhang

Guo

et al. 2021

Sensors

View full text Add to dashboard Cite

In the past few decades, biosensors have been gradually developed for the rapid detection and monitoring of human diseases. Recently, functional nucleic-acid (FNA) biosensors have attracted the attention of scholars due to a series of advantages such as high stability and strong specificity, as well as the significant progress they have made in terms of biomedical applications. However, there are few reports that systematically and comprehensively summarize its working principles, classification and application. In this review, we primarily introduce functional modes of biosensors that combine functional nucleic acids with different signal output modes. In addition, the mechanisms of action of several media of the FNA biosensor are introduced. Finally, the practical application and existing problems of FNA sensors are discussed, and the future development directions and application prospects of functional nucleic acid sensors are prospected.

show abstract

Characteristics and application of S1–P1 nucleases in biotechnology and medicine

Cited by 18 publications

References 134 publications

Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4

Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4

DNA Origami Post‐Processing by CRISPR‐Cas12a

Recent Advances on Functional Nucleic-Acid Biosensors

Contact Info

Product

Resources

About