| 2. |
- Wacker, A, et al.
(author)
-
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy
- 2020
-
In: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 48:22, s. 12415-12435
-
Journal article (peer-reviewed)abstract
- The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5′ end, the ribosomal frameshift segment and the 3′-untranslated region (3′-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.
|
|
| 3. |
- Dogan, B, et al.
(author)
-
Subgingival microflora in Turkish patients with periodontitis.
- 2003
-
In: Journal of Periodontology. - : Wiley. - 0022-3492 .- 1943-3670. ; 74:6, s. 803-814
-
Journal article (peer-reviewed)abstract
- BACKGROUND: No information exists on periodontitis-associated subgingival microbiota from Turkey. We determined the occurrence, interspecies relationships, and clonal characteristics for a group of periodontal bacteria in a Turkish study population. METHODS: Subgingival microbial samples were obtained from patients with localized (LAgP, N = 18) or generalized (GAgP, N = 17) types of aggressive periodontitis, generalized chronic periodontitis (GCP, N = 14), and non-periodontitis subjects (N = 20). Culture methods were used to recover 6 periodontal bacterial species and yeasts, and a polymerase chain reaction technique was used to detect Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis. Intraspecies characterization of A. actinomycetemcomitans was carried out by serotyping and genotyping. RESULTS: All species, except for Micromonas micros (formerly Peptostreptococcus micros) occurred more frequently (P < 0.05) in periodontitis than non-periodontitis subjects. Detection frequencies for Tannerella forsythensis (formerly Bacteroides forsythus) and Campylobacter rectus differed among the periodontitis subgroups; the lowest frequency occurred in LAgP. The mean proportions of A. actinomycetemcomitans, P. gingivalis, and C. rectus were higher (P < 0.008) in GAgP than in non-periodontitis subjects. Significant positive associations were seen between 7 of the 22 possible combinations (P < 0.05). A. actinomycetemcomitans serotype c (34%) and non-serotypeable isolates (34%) were the most common antigenic types among the 305 strains analyzed. Eleven arbitrarily primed (AP)-PCR genotypes were distinguished among 273 isolates from 29 subjects. Yeasts were found in 23% of the 69 subjects. CONCLUSIONS: The results on the Turkish study population were generally in line with earlier reports on the occurrence and interspecies relationships of certain bacteria in periodontitis. However, A. actinomycetemcomitans was not overrepresented in LAgP, and the serotype distribution resembled that reported from the East. The high frequency of non-serotypeable isolates suggests local characteristics of the species.
|
|
