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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.

Show MeSH
PNA binding. DNA probes of identical sequence but different chirality were spotted onto microarrays and hybridized with a set of complementary oligomers that were fluorescently labelled. L-DNA and D-DNA oligomers hybridized only to their respective enantiomeric probe set. PNA oligomers, on the other hand, showed no discrimination between D- and L-form but bound specifically to complementary sequences in either conformation.
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fig4: PNA binding. DNA probes of identical sequence but different chirality were spotted onto microarrays and hybridized with a set of complementary oligomers that were fluorescently labelled. L-DNA and D-DNA oligomers hybridized only to their respective enantiomeric probe set. PNA oligomers, on the other hand, showed no discrimination between D- and L-form but bound specifically to complementary sequences in either conformation.

Mentions: Apart from oligonucleotides, we also synthesized a set of complementary PNA oligomers, each molecule again labelled with a fluorophore. Upon hybridization of the PNA molecules at high-stringency conditions, binding could be observed to both the complementary D- and L-DNA ZIP-code sequences (Figure 4). While D- and L-enantiomeric molecules of complementary sequence did not interact with each other, they both hybridized specifically to complementary PNA sequences.


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)

PNA binding. DNA probes of identical sequence but different chirality were spotted onto microarrays and hybridized with a set of complementary oligomers that were fluorescently labelled. L-DNA and D-DNA oligomers hybridized only to their respective enantiomeric probe set. PNA oligomers, on the other hand, showed no discrimination between D- and L-form but bound specifically to complementary sequences in either conformation.
© Copyright Policy
Related In: Results  -  Collection

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

fig4: PNA binding. DNA probes of identical sequence but different chirality were spotted onto microarrays and hybridized with a set of complementary oligomers that were fluorescently labelled. L-DNA and D-DNA oligomers hybridized only to their respective enantiomeric probe set. PNA oligomers, on the other hand, showed no discrimination between D- and L-form but bound specifically to complementary sequences in either conformation.
Mentions: Apart from oligonucleotides, we also synthesized a set of complementary PNA oligomers, each molecule again labelled with a fluorophore. Upon hybridization of the PNA molecules at high-stringency conditions, binding could be observed to both the complementary D- and L-DNA ZIP-code sequences (Figure 4). While D- and L-enantiomeric molecules of complementary sequence did not interact with each other, they both hybridized specifically to complementary PNA sequences.

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