Prevalence of six periodontal pathogens detected by DNA probe method in HIV vs non-HIV periodontitis

ABSTRACT Background In clinical microbiology several techniques have been used to identify bacteria. Recently, Deoxyribonucleic acid (DNA)-based techniques have been introduced to detect human microbial pathogens in periodontal diseases. Deoxyribonucleic acid probes can detect bacteria at a very low level if we compared with the culture methods. These probes have shown rapid and cost-effective microbial diagnosis, good sensitivity and specificity for some periodontal pathogens in cases of severe periodontitis. Materials and methods Eighty-five patients were recruited for the study. Twenty-one subjects ranging between 22 and 48 years of age fulfilled the inclusion and exclusion criteria. Seventy-eight samples became available for DNA probe analysis from the deepest pockets in each quadrant. Results All 21 patients showed positive results for Prevotella intermedia; also, Prevotella gingivalis was identified in 19 subjects, Aggregatibacter actinomycetemcomitans in 6 subjects. P. intermedia was diagnosed positive in 82% of the subgingival samples taken, 79% for P. gingivalis, and 23% for A. actinomycetemcomitans. Conclusion This study shows a high frequency of putative periodontal pathogens by using DNA probe technology, which is semi-quantitative in this study. Deoxyribonucleic acid probes can detect bacteria at very low level about 103 which is below the detection level of culture methods. The detection threshold of cultural methods. Clinical significance The three types of bacteria can be detected rapidly with high sensitivity by using the DNA probe by general practitioners, and thus can help in the diagnosis process and the treatment. How to cite this article Yahfoufi ZAL, Hadchiti W, Berberi A. Deoxyribonucleic Acid Probes Analyses for the Detection of Periodontal Pathogens. J Contemp Dent Pract 2015;16(9): 727-732.

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Application of solid-phase DNA probe method with cleavage by deoxyribozyme for analysis of long non-coding RNAs

The Journal of Biochemistry ◽

10.1093/jb/mvaa048 ◽

2020 ◽

Vol 168 (3) ◽

pp. 273-283

Author(s):

Shizuka Arakawa ◽

Kohsuke Kamizaki ◽

Yusuke Kuwana ◽

Naruki Kataoka ◽

Chieko Naoe ◽

...

Keyword(s):

16S Rrna ◽

Messenger Rna ◽

Solid Phase ◽

Dna Probe ◽

Probe Method ◽

Modified Nucleosides ◽

Spectrometric Analysis ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Long Non Coding Rna

Abstract The solid-phase DNA probe method is a well-established technique for tRNA purification. We have applied this method for purification and analysis of other non-coding RNAs. Three columns for purification of tRNAPhe, transfer-messenger RNA (tmRNA) and 16S rRNA from Thermus thermophilus were connected in tandem and purifications were performed. From each column, tRNAPhe, tmRNA and 16S rRNA could be purified in a single step. This is the first report of purification of native tmRNA from T. thermophilus and the purification demonstrates that the solid-phase DNA probe method is applicable to non-coding RNA, which is present in lower amounts than tRNA. Furthermore, if a long non-coding RNA is cleaved site-specifically and the fragment can be purified by the solid-phase DNA probe method, modified nucleosides in the long non-coding RNA can be analysed. Therefore, we designed a deoxyribozyme (DNAzyme) to perform site-specific cleavage of 16S rRNA, examined optimum conditions and purified the resulting RNA fragment. Sequencing of complimentary DNA and mass spectrometric analysis revealed that the purified RNA corresponded to the targeted fragment of 16S rRNA. Thus, the combination of DNAzyme cleavage and purification using solid-phase DNA probe methodology can be a useful technique for analysis of modified nucleosides in long non-coding RNAs.

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