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Utilising the left-helical conformation of L-DNA for analysing different marker types on a single universal microarray platform.

Hauser NC, Martinez R, Jacob A, Rupp S, Hoheisel JD, Matysiak S - Nucleic Acids Res. (2006)

Bottom Line: Because of its chiral difference, L-DNA does not bind to its naturally occurring D-DNA counterpart, however.Typical results for the measurement of transcript level variations, genotypic differences and DNA-protein interactions are presented.However, on the basis of the characteristic features of L-DNA, also other applications of this molecule type are discussed.

View Article: PubMed Central - PubMed

Affiliation: Genomics-Proteomics-Systemsbiology, Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik Nobelstrasse 12, 70569 Stuttgart, Germany. nicole.hauser@igb.fraunhofer.de

ABSTRACT
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and selectivity as D-DNA but form a left-helical double-helix. Because of its chiral difference, L-DNA does not bind to its naturally occurring D-DNA counterpart, however. We analysed some of the properties that are typical for L-DNA. For all the differences, L-DNA is chemically compatible with the D-form of DNA, so that chimeric molecules can be synthesized. We take advantage of the characteristics of L-DNA toward the establishment of a universal microarray that permits the analysis of different kinds of molecular diagnostic information in a single experiment on a single platform, in various combinations. Typical results for the measurement of transcript level variations, genotypic differences and DNA-protein interactions are presented. However, on the basis of the characteristic features of L-DNA, also other applications of this molecule type are discussed.

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Related in: MedlinePlus

Combined assay of an analysis of transcription factor binding and SNP-typing. Assays that had been done separately before were performed simultaneously and analysed by a hybridization to a single L-DNA ZIP-code microarray. The top and bottom rows represent Cy3-labelled oligonucleotides, which had been placed to the surface as positional controls. While the mere signal intensity is informative about the interaction of NF-kappaB and DNA, double-labelling had been performed for the SNP-typing. Yellow spots indicate heterozygous samples (Int-22, SNP-9), red signals the presence of a dG in both alleles (SNP-2, SNP-10), while green spots represent homozygous dA sequences. In addition, a Cy5-labelled ICT had been spiked in, hybridizing to a row of ICP oligonucleotides.
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fig9: Combined assay of an analysis of transcription factor binding and SNP-typing. Assays that had been done separately before were performed simultaneously and analysed by a hybridization to a single L-DNA ZIP-code microarray. The top and bottom rows represent Cy3-labelled oligonucleotides, which had been placed to the surface as positional controls. While the mere signal intensity is informative about the interaction of NF-kappaB and DNA, double-labelling had been performed for the SNP-typing. Yellow spots indicate heterozygous samples (Int-22, SNP-9), red signals the presence of a dG in both alleles (SNP-2, SNP-10), while green spots represent homozygous dA sequences. In addition, a Cy5-labelled ICT had been spiked in, hybridizing to a row of ICP oligonucleotides.

Mentions: Combining different kinds of assays on a single chip platform could be advantageous for the application of microarrays as a diagnostic tool. Usually, the number of really informative molecular markers is limited. However, such molecules exist at several molecular levels. We performed a combined analysis of the transcription factor binding assays and SNP-typing (Figure 9). For the former only one label was required, while two differently labelled dideoxynucleotides (ddGTP and ddATP) were used in the latter experiment. As a control for both labelling and hybridization, also the ICT was added to the hybridization mixture. Although detection was done in a single scanning process, data analysis is individual. The occurrence of transcription factor binding could be determined from the variation of signal intensity. Alternatively, the actual signal intensity is irrelevant for the SNP-typing. Base calling depends merely on the ratio of incorporation of the two dideoxynucleotides.


Utilising the left-helical conformation of L-DNA for analysing different marker types on a single universal microarray platform.

Hauser NC, Martinez R, Jacob A, Rupp S, Hoheisel JD, Matysiak S - Nucleic Acids Res. (2006)

Combined assay of an analysis of transcription factor binding and SNP-typing. Assays that had been done separately before were performed simultaneously and analysed by a hybridization to a single L-DNA ZIP-code microarray. The top and bottom rows represent Cy3-labelled oligonucleotides, which had been placed to the surface as positional controls. While the mere signal intensity is informative about the interaction of NF-kappaB and DNA, double-labelling had been performed for the SNP-typing. Yellow spots indicate heterozygous samples (Int-22, SNP-9), red signals the presence of a dG in both alleles (SNP-2, SNP-10), while green spots represent homozygous dA sequences. In addition, a Cy5-labelled ICT had been spiked in, hybridizing to a row of ICP oligonucleotides.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1636439&req=5

fig9: Combined assay of an analysis of transcription factor binding and SNP-typing. Assays that had been done separately before were performed simultaneously and analysed by a hybridization to a single L-DNA ZIP-code microarray. The top and bottom rows represent Cy3-labelled oligonucleotides, which had been placed to the surface as positional controls. While the mere signal intensity is informative about the interaction of NF-kappaB and DNA, double-labelling had been performed for the SNP-typing. Yellow spots indicate heterozygous samples (Int-22, SNP-9), red signals the presence of a dG in both alleles (SNP-2, SNP-10), while green spots represent homozygous dA sequences. In addition, a Cy5-labelled ICT had been spiked in, hybridizing to a row of ICP oligonucleotides.
Mentions: Combining different kinds of assays on a single chip platform could be advantageous for the application of microarrays as a diagnostic tool. Usually, the number of really informative molecular markers is limited. However, such molecules exist at several molecular levels. We performed a combined analysis of the transcription factor binding assays and SNP-typing (Figure 9). For the former only one label was required, while two differently labelled dideoxynucleotides (ddGTP and ddATP) were used in the latter experiment. As a control for both labelling and hybridization, also the ICT was added to the hybridization mixture. Although detection was done in a single scanning process, data analysis is individual. The occurrence of transcription factor binding could be determined from the variation of signal intensity. Alternatively, the actual signal intensity is irrelevant for the SNP-typing. Base calling depends merely on the ratio of incorporation of the two dideoxynucleotides.

Bottom Line: Because of its chiral difference, L-DNA does not bind to its naturally occurring D-DNA counterpart, however.Typical results for the measurement of transcript level variations, genotypic differences and DNA-protein interactions are presented.However, on the basis of the characteristic features of L-DNA, also other applications of this molecule type are discussed.

View Article: PubMed Central - PubMed

Affiliation: Genomics-Proteomics-Systemsbiology, Fraunhofer-Institut für Grenzflächen- und Bioverfahrenstechnik Nobelstrasse 12, 70569 Stuttgart, Germany. nicole.hauser@igb.fraunhofer.de

ABSTRACT
L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and selectivity as D-DNA but form a left-helical double-helix. Because of its chiral difference, L-DNA does not bind to its naturally occurring D-DNA counterpart, however. We analysed some of the properties that are typical for L-DNA. For all the differences, L-DNA is chemically compatible with the D-form of DNA, so that chimeric molecules can be synthesized. We take advantage of the characteristics of L-DNA toward the establishment of a universal microarray that permits the analysis of different kinds of molecular diagnostic information in a single experiment on a single platform, in various combinations. Typical results for the measurement of transcript level variations, genotypic differences and DNA-protein interactions are presented. However, on the basis of the characteristic features of L-DNA, also other applications of this molecule type are discussed.

Show MeSH
Related in: MedlinePlus