Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids


Synthetic molecules that recognize specific sequences within cellular DNA are potentially powerful tools for investigating chromosome structure and function. Here, we designed antigene peptide nucleic acids (agPNAs) to target the transcriptional start sites for the human progesterone receptor B (hPR-B) and A (hPR-A) isoforms at sequences predicted to be single-stranded within the open complex of chromosomal DNA. We found that the agPNAs were potent inhibitors of transcription, showing for the first time that synthetic molecules can recognize transcription start sites inside cells. Breast cancer cells treated with agPNAs showed marked changes in morphology and an unexpected relationship between the strictly regulated levels of hPR-B and hPR-A. We confirmed these phenotypes using siRNAs and antisense PNAs, demonstrating the power of combining antigene and antisense strategies for gene silencing. agPNAs provide a general approach for controlling transcription initiation and a distinct option for target validation and therapeutic development.

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Figure 1: Schematic showing the effect of agPNAs on transcription.
Figure 2: Effect of agPNAs on expression of hPR.
Figure 3: Dose-response profiles for inhibition of hPR expression.
Figure 4: Graphical analysis of the linkage between levels of hPR-B and hPR-A in transfected T47D cells.
Figure 5: Effect of inhibiting hPR expression on cell morphology and ezrin expression.


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This work was supported by the US National Institutes of Health (NIGMS 60642 and 73042 to D.R.C. and P01 HD011149 to C.R.M.) and the Robert A. Welch Foundation (I-1244).

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Correspondence to David R Corey.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Effect of estradiol treatment on the ability of agPNAs to inhibit hPR gene expression. (PDF 282 kb)

Supplementary Methods (PDF 79 kb)

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Janowski, B., Kaihatsu, K., Huffman, K. et al. Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids. Nat Chem Biol 1, 210–215 (2005).

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