Tandem trimer pyrrole-imidazole polyamide probes targeting 18 base pairs in human telomere sequences.

Tandem trimer pyrrole–imidazole polyamide probes targeting 18 base pairs in human telomere sequences† †Electronic supplementary information (ESI) available: Materials and methods, sequences of ODN-1 to 5, mass spectra and analytical HPLC profiles of the compounds TH59, TT59, TAMRA TH59 and TAMRA TT59, the UV-visible absorption and fluorescence spectra of probes TAMRA TH59 and TAMRA TT59, SPR sensorgrams of TH59 and TT59, additional images of telomeres. See DOI: 10.1039/c4sc03755c Click here for additional data file.

Telomere Visualization in Tissue Sections using Pyrrole–Imidazole Polyamide Probes

Pyrrole-Imidazole (PI) polyamides bind to specific DNA sequences in the minor groove with high affinity. Specific DNA labeling by PI polyamides does not require DNA denaturation with harsh treatments of heat and formamide and has the advantages of rapid and less disruptive processing. Previously, we developed tandem hairpin PI polyamide probes (TH59 series), which label telomeres in cultured ce...

Synthetic pyrrole-imidazole polyamide inhibits expression of the human transforming growth factor-beta1 gene.

Pyrrole-imidazole (Py-Im) polyamides can bind to the predetermined base pairs in the minor groove of double-helical DNA with high affinity. These synthetic small molecules can interfere with transcription factor-DNA interaction and inhibit or activate the transcription of corresponding genes. In the present study, we designed and synthesized a Py-Im polyamide to target -545 to -539 base pairs o...

Effects of the A.T/T.A degeneracy of pyrrole--imidazole polyamide recognition in the minor groove of DNA.

Pairing rules have been developed to predict the sequence specificity of minor groove binding polyamides containing pyrrole (Py) and imidazole (Im) amino acids. An Im/Py pair distinguishes G.C from C.G and both of these from A.T/T.A base pairs. A Py/Py pair appears not to distinguish A.T from T.A base pairs. To test the extent of this degeneracy, the affinity and binding orientation of the hair...

Extension of Sequence-Specific Recognition in the Minor Groove of DNA by Pyrrole-Imidazole Polyamides to 9-13 Base Pairs

The sequence-specific recognition of the minor groove of DNA by pyrrole-imidazole polyamides has been extended to 9-13 base pairs (bp). Four polyamides, ImPyPy-Py-PyPyPy-Dp, ImPyPy-G-PyPyPy-Dp, ImPyPyâ-PyPyPy-Dp, and ImPyPy-γ-PyPyPy-Dp (Im ) N-methylimidazole, Py ) N-methylpyrrole, Dp ) N,Ndimethylaminopropylamide, G ) glycine, â ) â-alanine, and γ ) γ-aminobutyric acid), were synthesized and c...