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DNA watermarks in non-coding regulatory sequences.

Heider D, Pyka M, Barnekow A - BMC Res Notes (2009)

Bottom Line: In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity.Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly.Therefore, we do not recommend integrating watermark sequences into regulatory regions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Experimental Tumorbiology, University of Münster, Badestr, 9, D-48149 Münster, Germany. dominik.heider@uni-due.de

ABSTRACT

Background: DNA watermarks can be applied to identify the unauthorized use of genetically modified organisms. It has been shown that coding regions can be used to encrypt information into living organisms by using the DNA-Crypt algorithm. Yet, if the sequence of interest presents a non-coding DNA sequence, either the function of a resulting functional RNA molecule or a regulatory sequence, such as a promoter, could be affected. For our studies we used the small cytoplasmic RNA 1 in yeast and the lac promoter region of Escherichia coli.

Findings: The lac promoter was deactivated by the integrated watermark. In addition, the RNA molecules displayed altered configurations after introducing a watermark, but surprisingly were functionally intact, which has been verified by analyzing the growth characteristics of both wild type and watermarked scR1 transformed yeast cells. In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity.

Conclusion: Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly. Therefore, we do not recommend integrating watermark sequences into regulatory regions.

No MeSH data available.


Related in: MedlinePlus

Secondary structure of the wild type scR1 and the watermarked scR1. The secondary structure predictions were performed using the ViennaRNA-1.5 web interface. The 3D model was created using Blender. A: wild type scR1 of Saccharomyces cerevisiae; B: watermarked scR1 (see section methods)
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Figure 1: Secondary structure of the wild type scR1 and the watermarked scR1. The secondary structure predictions were performed using the ViennaRNA-1.5 web interface. The 3D model was created using Blender. A: wild type scR1 of Saccharomyces cerevisiae; B: watermarked scR1 (see section methods)

Mentions: In 2001, Dieci et al. showed that after transformation of YRA130 ΔscR1 yeast cells with the wild type scR1 Yep352 plasmid, a normal division rate was achieved and the wild type phenotype could be rescued [12]. For our studies we transformed the YRA130 ΔscR1 yeast cells with the Yep352 plasmid containing a watermarked scR1 gene (Yep352-SCR1-TB). The watermark sequence was integrated into the wild type scR1 gene starting at position 471 (see mutagenic primer sequences). The secondary structure predictions of the watermarked scR1 using the ViennaRNA-1.5 web interface revealed significant changes within the secondary structure compared to the structure of the wild type scR1 (Figure 1) [22]. The 3D model was created using Blender .


DNA watermarks in non-coding regulatory sequences.

Heider D, Pyka M, Barnekow A - BMC Res Notes (2009)

Secondary structure of the wild type scR1 and the watermarked scR1. The secondary structure predictions were performed using the ViennaRNA-1.5 web interface. The 3D model was created using Blender. A: wild type scR1 of Saccharomyces cerevisiae; B: watermarked scR1 (see section methods)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2713970&req=5

Figure 1: Secondary structure of the wild type scR1 and the watermarked scR1. The secondary structure predictions were performed using the ViennaRNA-1.5 web interface. The 3D model was created using Blender. A: wild type scR1 of Saccharomyces cerevisiae; B: watermarked scR1 (see section methods)
Mentions: In 2001, Dieci et al. showed that after transformation of YRA130 ΔscR1 yeast cells with the wild type scR1 Yep352 plasmid, a normal division rate was achieved and the wild type phenotype could be rescued [12]. For our studies we transformed the YRA130 ΔscR1 yeast cells with the Yep352 plasmid containing a watermarked scR1 gene (Yep352-SCR1-TB). The watermark sequence was integrated into the wild type scR1 gene starting at position 471 (see mutagenic primer sequences). The secondary structure predictions of the watermarked scR1 using the ViennaRNA-1.5 web interface revealed significant changes within the secondary structure compared to the structure of the wild type scR1 (Figure 1) [22]. The 3D model was created using Blender .

Bottom Line: In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity.Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly.Therefore, we do not recommend integrating watermark sequences into regulatory regions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Experimental Tumorbiology, University of Münster, Badestr, 9, D-48149 Münster, Germany. dominik.heider@uni-due.de

ABSTRACT

Background: DNA watermarks can be applied to identify the unauthorized use of genetically modified organisms. It has been shown that coding regions can be used to encrypt information into living organisms by using the DNA-Crypt algorithm. Yet, if the sequence of interest presents a non-coding DNA sequence, either the function of a resulting functional RNA molecule or a regulatory sequence, such as a promoter, could be affected. For our studies we used the small cytoplasmic RNA 1 in yeast and the lac promoter region of Escherichia coli.

Findings: The lac promoter was deactivated by the integrated watermark. In addition, the RNA molecules displayed altered configurations after introducing a watermark, but surprisingly were functionally intact, which has been verified by analyzing the growth characteristics of both wild type and watermarked scR1 transformed yeast cells. In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity.

Conclusion: Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly. Therefore, we do not recommend integrating watermark sequences into regulatory regions.

No MeSH data available.


Related in: MedlinePlus