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Fluorogenic thiazole orange TOTFO probes stabilise parallel DNA triplexes at pH 7 and above.

ABSTRACT: The instability of DNA triplexes particularly at neutral pH and above severely limits their applications. Here, we demonstrate that the introduction of a thiazole orange (TO) intercalator onto a thymine nucleobase in triplex forming oligonucleotides (TFOs) resolves this problem. The stabilising effects are additive; multiple TO units produce nanomolar duplex binding and triplex stability can surpass that of the underlying duplex. In one example, a TFO containing three TO units increased the triplex melting temperature at pH 7 by a remarkable 50 °C relative to the unmodified triplex. Notably, TO intercalation promotes TFO binding to target sequences other than pure polypurine tracts by the use of 5-(1-propynyl)cytosine (pC) against C:G inversions. By overcoming the instability of triplexes across a broad range of pH and sequence contexts, these very simple 'TOTFO' probes could expand triplex applications into many areas including diagnostics and cell imaging.

SUBMITTER: Walsh S

PROVIDER: S-EPMC6182420 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Fluorogenic thiazole orange TOTFO probes stabilise parallel DNA triplexes at pH 7 and above.

Walsh Sarah S El-Sagheer Afaf Helmy AH Brown Tom T

Chemical science 20180801 39

The instability of DNA triplexes particularly at neutral pH and above severely limits their applications. Here, we demonstrate that the introduction of a thiazole orange (TO) intercalator onto a thymine nucleobase in triplex forming oligonucleotides (TFOs) resolves this problem. The stabilising effects are additive; multiple TO units produce nanomolar duplex binding and triplex stability can surpass that of the underlying duplex. In one example, a TFO containing three TO units increased the trip ...[more]

PMID: 30393529

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