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BMC genomics2013; 14; 370; doi: 10.1186/1471-2164-14-370

A new genomic tool, ultra-frequently cleaving TaqII/sinefungin endonuclease with a combined 2.9-bp recognition site, applied to the construction of horse DNA libraries.

Abstract: Genomics and metagenomics are currently leading research areas, with DNA sequences accumulating at an exponential rate. Although enormous advances in DNA sequencing technologies are taking place, progress is frequently limited by factors such as genomic contig assembly and generation of representative libraries. A number of DNA fragmentation methods, such as hydrodynamic sharing, sonication or DNase I fragmentation, have various drawbacks, including DNA damage, poor fragmentation control, irreproducibility and non-overlapping DNA segment representation. Improvements in these limited DNA scission methods are consequently needed. An alternative method for obtaining higher quality DNA fragments involves partial digestion with restriction endonucleases (REases). Results: We constructed a horse genomic library and a deletion derivative library of the butyrylcholinesterase cDNA coding region using a novel method, based on TaqII, Thermus sp. family bifunctional enzyme exhibiting cofactor analogue specificity relaxation. We used sinefungin (SIN) - an S-adenosylmethionine (SAM) analogue with reversed charge pattern, and dimethylsulfoxide (DMSO), to convert the 6-bp recognition site TaqII (5'-GACCGA-3' [11/9]) into a theoretical 2.9-bp REase, with 70 shortened variants of the canonical recognition sequence detected. Because partial DNA cleavage is an inherent feature of the Thermus sp. enzyme family, this modified TaqII is uniquely suited to quasi-random library generation. Conclusions: In the presence of SIN/DMSO, TaqII REase is transformed from cleaving every 4096 bp on average to cleaving every 58 bp. TaqII SIN/DMSO thus extends the palette of available REase prototype specificities. This phenomenon, employed under partial digestion conditions, was applied to quasi-random DNA fragmentation. Further applications include high sensitivity probe generation and metagenomic DNA amplification.
Publication Date: 2013-06-01 PubMed ID: 23724933PubMed Central: PMC3681635DOI: 10.1186/1471-2164-14-370Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research paper presents a novel technique, using a bioengineered version of the restriction enzyme TaqII, to produce small and uniform fragments of DNA for genomic studies such as the creation of libraries and amplification of metagenomic DNA.

Restriction Enzymes in Genomics

  • The focus of the study is the field of genomics and metagenomics, two areas where DNA sequencing technologies are developing rapidly, generating huge quantities of sequence data.
  • However, the researchers identify problems related to the assembly of the entire genome (contig assembly) and the production of a representative library due to limitations in the current methods used to break the DNA into smaller pieces – methods such as hydrodynamic shearing, sonication, and DNase I fragmentation.
  • One alternative, and the focus of this research, is the use of restriction enzymes (REases) for DNA breakdown, which could result in higher quality fragments.

Modified TaqII and DNA Fragmentation

  • The team developed a new method to fragment DNA using a bioengineered version of the restriction enzyme TaqII, which originates from a family of bifunctional enzymes found in a bacterium called Thermus sp.
  • Through the use of sinefungin (SIN) and dimethylsulfoxide (DMSO), the traditional 6-base pair (bp) recognition site of TaqII is converted into a theoretical 2.9-bp site. This version of TaqII can recognise shorter DNA sequences and leads to the creation of more and smaller fragments.
  • Using this modified enzyme, they were able to construct a horse genomic library, along with a derivative library made up of DNA in the coding region of the butyrylcholinesterase gene.

Applications of the Study

  • The technique of partial DNA cleavage inherent in the modified TaqII enzyme makes it ideal for generating quasi-random libraries, an important tool in genomic research.
  • The presence of SIN/DMSO allows TaqII to cut DNA at approximately every 58 base pairs instead of every 4,096 base pairs as per the native version of the enzyme. This modifies the specificity of the enzyme and presents a more versatile tool for genomic studies.
  • According to the researchers, this method could also be used for the creation of high-sensitivity probes and amplification of metagenomic DNA, broadening its application in the scientific community.

Cite This Article

APA
Zylicz-Stachula A, Zolnierkiewicz O, Jasiecki J, Skowron PM. (2013). A new genomic tool, ultra-frequently cleaving TaqII/sinefungin endonuclease with a combined 2.9-bp recognition site, applied to the construction of horse DNA libraries. BMC Genomics, 14, 370. https://doi.org/10.1186/1471-2164-14-370

Publication

ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 14
Pages: 370

Researcher Affiliations

Zylicz-Stachula, Agnieszka
    Zolnierkiewicz, Olga
      Jasiecki, Jacek
        Skowron, Piotr M

          MeSH Terms

          • Adenosine / analogs & derivatives
          • Adenosine / chemistry
          • Animals
          • DNA Cleavage
          • Deoxyribonucleases, Type II Site-Specific / chemistry
          • Genomic Library
          • Genomics / methods
          • Horses / genetics
          • Substrate Specificity
          • Thermus / enzymology

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          Citations

          This article has been cited 6 times.
          1. Zebrowska J, Jezewska-Frackowiak J, Wieczerzak E, Kasprzykowski F, Zylicz-Stachula A, Skowron PM. Novel parameter describing restriction endonucleases: Secondary-Cognate-Specificity and chemical stimulation of TsoI leading to substrate specificity change. Appl Microbiol Biotechnol 2019 Apr;103(8):3439-3451.
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          2. Krefft D, Papkov A, Prusinowski M, Zylicz-Stachula A, Skowron PM. Randomized DNA libraries construction tool: a new 3-bp 'frequent cutter' TthHB27I/sinefungin endonuclease with chemically-induced specificity. BMC Genomics 2018 May 11;19(1):361.
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