Improvements in Bacterial Primers to Enhance Selective SSU rRNA Gene Amplification of Plant-associated Bacteria by Applying the LNA Oligonucleotide-PCR Clamping Technique

Ikenaga, Makoto; Katsuragi, Shohei; Handa, Yoshihiro; Katsumata, Hiroshi; Chishaki, Naoya; Kawauchi, Tomohiro; Sakai, Masao

doi:10.1264/jsme2.me18071

Cited by 15 publications

(8 citation statements)

References 28 publications

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“…Mixmers include the LNA and the other residues interspersed in different configurations throughout the sequence. LNA-containing oligomers have been used for diagnostics and other applications, as probes or primers for hybridization, amplification, mutagenesis, sequencing, and SNP genotyping [46,47,48,49,50,51,52,53], in addition to gene repair [54] and antisense drugs [13,41,42,55]. While the increased binding capacity is advantageous in many antisense applications, it can also be detrimental due to the formation of duplex structures that cannot be recognized as substrates by the enzymes recruited to degrade the target molecule.…”

Section: Lna—a Brief Overviewmentioning

confidence: 99%

Bridged Nucleic Acids Reloaded

2019

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Oligonucleotides are key compounds widely used for research, diagnostics, and therapeutics. The rapid increase in oligonucleotide-based applications, together with the progress in nucleic acids research, has led to the design of nucleotide analogs that, when part of these oligomers, enhance their efficiency, bioavailability, or stability. One of the most useful nucleotide analogs is the first-generation bridged nucleic acids (BNA), also known as locked nucleic acids (LNA), which were used in combination with ribonucleotides, deoxyribonucleotides, or other analogs to construct oligomers with diverse applications. However, there is still room to improve their efficiency, bioavailability, stability, and, importantly, toxicity. A second-generation BNA, BNANC (2′-O,4′-aminoethylene bridged nucleic acid), has been recently made available. Oligomers containing these analogs not only showed less toxicity when compared to LNA-containing compounds but, in some cases, also exhibited higher specificity. Although there are still few applications where BNANC-containing compounds have been researched, the promising results warrant more effort in incorporating these analogs for other applications. Furthermore, newer BNA compounds will be introduced in the near future, offering great hope to oligonucleotide-based fields of research and applications.

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Section: Lna—a Brief Overviewmentioning

confidence: 99%

Bridged Nucleic Acids Reloaded

2019

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“…High-throughput sequencing technology has greatly advanced our understanding of microbial ecology in various environments (19, 38). Culture-independent, high-throughput sequencing of the 16S rRNA gene fragment is most commonly performed (21, 60); however, other applications, such as (meta)genomics and (meta)transcriptomics, are also frequently used (19, 25, 38). Since pathogenic and non-pathogenic strains are both present within a genus/species ( e.g ., pathogenic E. coli ), it is difficult to identify the presence of pathogens in a sample by the high-throughput 16S rRNA gene sequencing approach alone.…”

Section: Metagenomics and Amplicon Sequencingmentioning

confidence: 99%

Ecology of Pathogens and Antibiotic-resistant Bacteria in Environments: Challenges and Opportunities

Ishii

2019

Microb. Environ.

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Various bacteria can cause human diseases. They spread directly from person to person or indirectly via various environmental matrixes, such as food and water. Major food-and waterborne pathogens include Campylobacter, Listeria, Salmonella, Shigella, Shiga toxin-producing Escherichia coli, Salmonella, Yersinia, and Vibrio (31). Most of these pathogens spread through the fecal-oral route. Their primary hosts include humans, farm animals (e.g., cows, pigs, and chickens), and wildlife (e.g., deer, birds). These hosts contribute to the spread of pathogens. For example, geese and other birds are known to harbor diverse Campylobacter (29, 40, 59) and Salmonella spp. (40). However, some of these pathogens also survive for long periods of time and even grow in environments such as water, soil, sediment, and algae (13, 22, 32), in many cases in association with or by forming biofilms (35, 36, 52). Since difficulties are associated with detecting various pathogens in a timely manner, the microbial quality of food and water has been monitored using so-called fecal indicator bacteria (FIB), such as E. coli and enterococci (22, 24). Although their primary habitats are the gastrointestinal tracts of warmblooded animals (18, 49), some FIB strains are more adapted to soil or other environments (22, 24, 37). Moreover, alternative FIB, such as Bacteroides, have been used to identify the occurrence of pathogens and their potential sources of contamination (28, 59). However, poor correlations have been reported between pathogen and FIB concentrations (23, 58), which limits the use of FIB for predicting the occurrence of pathogens. Some opportunistic pathogens, including Mycobacterium avium and Legionella pneumophila, are not of a fecal origin. These opportunistic pathogens use environments such as water distribution systems (11, 14, 15) and showerhead biofilms (12) as their primary habitats, and occasionally infect humans to cause diseases. Furthermore, various environmental bacteria have been reported as emerging pathogens. Among these, Arcobacter spp. are of great interest because this genus is frequently and abundantly detected in many wastewater treatment plants (10, 50). This genus is phylogenetically closely related to Campylobacter, but is metabolically more versatile and can grow at relatively low temperatures and with a wider range of O 2 concentrations (9). Some members of Arcobacter have also been reported to form symbiotic relationships with protists (16). A better understanding of the ecology of these environmental pathogens is essential for preventing their occurrence and spread (39, 47).

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“…Mixmers include the LNA and the other residues interspersed in different configurations throughout the sequence. LNAcontaining oligomers have been used for diagnostics and other applications as probes or primers for hybridization, amplification, mutagenesis, sequencing, and SNP genotyping [39][40][41][42][43][44][45][46], in addition to gene repair [47] and antisense drugs [9,34,35,48]. While the increased binding capacity is advantageous in many antisense applications, it can also be detrimental due to formation of duplex structures that cannot be recognized as substrates by the enzymes recruited to degrade the target molecule.…”

Section: Lna -A Brief Overviewmentioning

confidence: 99%

Bridged Nucleic Acids Reloaded

Soler-Bistué

Zorreguieta

Tolmasky

2019

Preprint

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Oligonucleotides are key compounds widely used for research, diagnostics, and therapeutics. The rapid increase in oligonucleotide-based applications, together with the progress in nucleic acids research, led to the design of nucleotide analogs that when being part of these oligomers enhance their efficiency, bioavailability, or stability. One of the most useful nucleotide analogs are the first-generation bridge nucleic acids (BNA), also known as locked nucleic acids (LNA), which were used in combination with ribonucleotides, deoxyribonucleotides, or other analogs to construct oligomers with diverse applications. However, there is still room to improve their efficiency, bioavailability, stability, and, importantly, toxicity. A second generation BNA, BNANC (2'-O,4'-aminoethylene bridged nucleic acid), has been recently made available. Oligomers containing these analogs not only showed less toxicity when compared to LNA-containing compounds but in some cases also exhibited higher specificity. Although there are still few applications where BNANC-containing compounds were researched, the results are very promising warranting more efforts in incorporating these analogs for other applications. Furthermore, newer BNA compounds will be introduced in the near future offering great hope to oligonucleotide-based fields of research and applications.

show abstract

Improvements in Bacterial Primers to Enhance Selective SSU rRNA Gene Amplification of Plant-associated Bacteria by Applying the LNA Oligonucleotide-PCR Clamping Technique

Cited by 15 publications

References 28 publications

Bridged Nucleic Acids Reloaded

Bridged Nucleic Acids Reloaded

Ecology of Pathogens and Antibiotic-resistant Bacteria in Environments: Challenges and Opportunities

Bridged Nucleic Acids Reloaded

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