A DNA probe specific to Streptococcus sobrinus

Reverse transcription and polymerase chain reaction: principles and applications in dentistry

Various molecular biology techniques have become available in the last few years. One of the most revolutionary of these techniques regarding nucleic acid analysis is the polymerase chain reaction (PCR), which was first described in 1985. This method relies on the exponential amplification of specific DNA fragments, resulting in millions of copies that can serve as templates for different kinds of analyses. PCR can be preceded by a reverse transcription (RT) reaction in order to produce cDNA from RNA (RT-PCR). RT-PCR provides the possibility to assess gene transcription in cells or tissues. PCR and RT-PCR techniques have been instrumental in dental research, and show potential to be used for diagnosis as well as for treatment and prevention of many diseases (dental caries, periodontal disease, endodontic infections and oral cancer). Compared to other traditional methodologies, PCR and RT-PCR show many advantages including high specificity, sensitivity, and speed. Since PCR and RT-PCR are relatively new techniques and are not available to most students and professionals involved with dentistry, the aim of this work is to present the details of these techniques as well as dental literature reports in which they were used.

Identification of Streptococcus sanguinis with a PCR-generated species-specific DNA probe

The objective of the present study was to design a PCR-generated DNA probe and determine the specificity of the probe for the identification of clinical isolates of Streptococcus sanguinis. To do this, we examined over 200 arbitrarily primed PCR (AP-PCR) amplicon patterns obtained with DNA from clinical isolates of S. sanguinis. A 1.6-kb DNA amplicon that was common to all AP-PCR profiles was extracted from agarose gels and then cloned and sequenced. A search for a similar sequence in the GenBank database with the BLASTN program revealed that the 1.6-kb DNA fragment comprised an intergenic region between two housekeeping genes, uncC (proton-translocating ATPase) and murA (UDP-N-acetylglucosamine enolpyruvyl transferase). Three digoxigenin-labeled DNA probes were synthesized on the basis of the sequence of the 1.6-kb fragment: the sequence of probe SSA-1 contained the proton-translocating ATPase (uncC) and the entire intergenic region, the sequence of probe SSA-2 contained only the intergenic region, and the sequence of probe SSA-3 contained an internal region of the murA gene. Dot blot hybridization showed that the three probes displayed signals for hybridization to both S. sanguinis strain ATCC 10556 and the S. sanguinis clinical isolates. Probe SSA-1, however, hybridized to DNA from S. oralis and S. mitis. Probe SSA-3 hybridized to DNA from S. gordonii, S. mitis, S. oralis, S. parasanguinis, and S. vestibularis. The probe SSA-2-specific intergenic region appeared to be specific for S. sanguinis. The results from this study suggest that probe SSA-2 may serve as a species-specific DNA probe for the identification of clinical isolates of S. sanguinis.

Species-specific DNA probe for the detection of Porphyromonas gingivalis from adult Chinese periodontal patients and healthy subjects

BACKGROUND

It has been reported that Porphyromonas gingivalis is closely associated with chronic periodontitis and its detection has been recommended as a routine marker for periodontal diagnosis. The purpose of this study was to evaluate the sensitivity and specificity of a DNA probe to detect P. gingivalis in adult Chinese periodontitis patients as well as to find a rapid and convenient method to detect P. gingivalis in clinical practice.

METHODS

A total of 26 bacterial strains (20 reference strains and 6 clinical isolates) were collected, of which 5 were P. gingivalis and 21 were heterologous species. A DNA fragment of 542 bp, which encodes the fimbriae subunit protein (fimA) of P. gingivalis, was obtained by polymerase chain reaction (PCR) and molecular cloning techniques and used to construct the DNA probe, labeled with 32P or with digoxigenin. The constructed DNA probe was used to detect P. gingivalis in specimens collected from the periodontal pockets of 100 patients clinically confirmed with chronic periodontitis. One hundred periodontally healthy persons served as a control group.

RESULTS

Positive reactions were seen in all 5 strains of P. gingivalis while no visible reaction was found in other species. The DNA probe was capable of detecting as few as 100 P. gingivalis cells in samples. A significant difference in the positive rates of P. gingivalis between the periodontitis patients and the control group was found (P<0.01). In addition, the amount of detected P. gingivalis was positively correlated with the extent of tooth mobility, depth of periodontal pockets, and patient age (P<0.01).

CONCLUSION

The DNA probe is specific and sensitive for the detection of P. gingivalis in chronic periodontitis specimens and may be a suitable method for the clinical diagnosis of chronic periodontitis.

Nucleotide sequence and molecular characterization of a dextranase gene from Streptococcus downei

DNA fragments encoding the Streptococcus downei dextranase were amplified by PCR and inverse PCR based on a comparison of the dextranase gene (dex) sequences from S. sobrinus, S. mutans, and S. salivarius, and the complete nucleotide sequence of the S. downei dex was determined. An open reading frame (ORF) of dex was 3,891 bp long. It encoded a dextranase protein (Dex) consisting of 1,297 amino acids with a molecular mass of 139,743 Da and an isoelectric point of 4.49. The deduced amino acid sequence of S. downei Dex had homology to those of S. sobrinus, S. mutans and S. salivanus Dex in the conserved region (made of about 540 amino acid residues). DNA hybridization analysis showed that a dex DNA probe of S. downei hybridized to the chromosomal DNA of S. sobrinus as well as that of S. downei, but did not to other species of mutans streptococci. The C terminus of the S. downei Dex had a membrane-anchor region which has been reported as a common structure of C termini of both the S. mutans and S. sobrinus Dex. The recombinant plasmid which harbored the dex ORF of S. downei produced a recombinant Dex enzyme in Escherichia coli cells. The analysis of the recombinant enzyme on SDS-PAGE containing blue dextran showed multiple active forms as well as dextranases of S. mutans, S. sobrinus and S. salivarius.

Identification of mutans streptococcal species by the PCR products of the dex genes

A pair of polymerase chain reaction (PCR) primers was designed on the basis of the nucleotide sequence homology of dextranase genes (dex) of Streptococcus mutans, S. sobrinus and S. downei. The primer pair amplified a 530-bp DNA fragment on the dex genes of mutans streptococcal species: S. mutans, S. sobrinus, S. downei, S. rattus and S. cricetus. HaeIII digestion of the 530-bp fragments generated species-specific subfragments, which were easily distinguishable from each other by agarose gel electrophoresis. These results suggest that the PCR-amplification of the dex gene followed by the HaeIII digestion is useful for rapid identification of the five species of mutans streptococci.

Identification of Streptococcus salivarius by PCR and DNA probe

AIMS

To establish species-specific PCR and DNA probe methods for Streptococcus salivarius and to clarify the distribution of dextranase in oral isolates of Strep. salivarius.

METHODS AND RESULTS

A pair of PCR primers and a DNA probe were designed based on the nucleotide sequence of the dextranase gene of Strep. salivarius JCM5707. Both the PCR primer and the DNA probe specifically detected Strep. salivarius but none of the other oral streptococci (23 strains of 13 species). The primer and the probe were capable of detecting 1 pg and 1 ng of the genomic DNA, respectively, purified from Strep. salivarius JCM5707. All oral isolates (130 strains from 12 subjects) of Strep. salivarius from human saliva were positive by both methods.

CONCLUSION

The present PCR and DNA probe methods are highly specific to Strep. salivarius and are useful for the its detection and identification of this bacterium. The dextranase widely distributes among oral isolates of Strep. salivarius.

SIGNIFICANCE AND IMPACT OF THE STUDY

The DNA sequence of a dextranase gene present in the genome of Strep. salivarius is useful as the target DNA of the species-specific PCR and DNA probe.