Journal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
Volume 127, Issue 47, Pages 16685-16691Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ja054650k
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Funding
- NIGMS NIH HHS [F32 GM-19788, GM-27681] Funding Source: Medline
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Fluorescent methods to detect specific double-stranded DNA sequences without the need for denaturation may be useful in the field of genetics. Three hairpin pyrrole-imidazole polyamides 2-4 that target their respective sequences 5'-WGGGWW-3', 5'-WGGCCW-3', and 5'-WGWWCW-3'(W = A or T) were conjugated to thiazole orange dye at the C-termini to examine their fluorescence properties in the presence and absence of match duplex DNA. The conjugates fluoresce weakly in the absence of DNA but showed significant enhancement (> 1000-fold) upon the addition of 1 equiv of match DNA and only slight enhancement with the addition of mismatch DNA. The polyamide-dye conjugates bound specific DNA sequences with high affinity (K-a > 10(8) M-1) and unwound the DNA duplex through intercalation (unwinding angle, Phi, similar to 8 degrees). This new class of polyamides provides a method to specifically detect DNA sequences without denaturation.
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