Academic
Publications
Extending the Language of DNA Molecular Recognition by Polyamides:  Unexpected Influence of Imidazole and Pyrrole Arrangement on Binding Affinity and Specificity

Extending the Language of DNA Molecular Recognition by Polyamides:  Unexpected Influence of Imidazole and Pyrrole Arrangement on Binding Affinity and

Extending the Language of DNA Molecular Recognition by Polyamides:  Unexpected Influence of Imidazole and Pyrrole Arrangement on Binding Affinity and Specificity   (Citations: 11)
BibTex | RIS | RefWorks Download
Journal: Journal of The American Chemical Society - J AM CHEM SOC , vol. 127, no. 2, pp. 742-750, 2005
Cumulative Annual
View Publication
The following links allow you to view full publications. These links are maintained by other sources not affiliated with Microsoft Academic Search.
    • ...Recently, our group has demonstrated that the arrangement of the imidazole (Im) and pyrrole (Py) moieties, and the inclusion of an N-terminal formamido (f ) group are crucial in the design of useful polyamides (15,16)...
    • ...In addition, the context of imidazole and pyrrole moieties within the triamide must be considered when designing polyamide-based DNA binding agents (15)...
    • ...Interestingly, f-ImPyIm exhibits one-order of magnitude better affinity for its cognate DNA than does distamycin A for AATT (15)...
    • ...However, f-ImIm exhibits a low binding affinity for DNA, which relates to low specificity among a variety of sequences (15) and, therefore, the f/Im may exhibit base pair selectivity in other environments...
    • ...SPR experiments were performed using either a BIACORE 2000 or 3000 instrument (Biacore AB) as described previously with the DNA hairpins shown in Figure 2B (15,16,27,29)...
    • ...Keq for f-ImPyIm with AGCT, CCGG and TCGA could not be determined because the association and dissociation rates were too fast, which is consistent with previous observations that faster kinetics correlate with lower binding affinities (15,23)...
    • ...b,c These values were taken from Refs (15,16), respectively...
    • ...Keq = (K1K2) 1/2 = [(k a1/kd1) · (ka2/kd2)] 1/2 . c K eq is calculated from steady-state measurements, see Table 1. d,eThese values were taken from Refs (15,16), respectively...
    • ...Previous work showed that the ‐ImPy‐ and ‐PyPy‐ central pairing elements have higher affinity and specificity for their Watson‐ Crick cognate sequences than do ‐PyIm‐ and ‐ImIm‐ (15); therefore, ‐PyIm‐ and ‐ImIm‐ were not used in this study...
    • ...New rules, pertaining to formamido groups, are now added to those already necessary in polyamide design (5,15)...
    • ...Prior work showed that the Im/Py pairings of the non-formylated ImPyPy recognize the G/C base pairs of a GTC containing DNA hairpin with � 25fold better affinity than DNA sequences that did not contain either GTC or GAC (15)...
    • ...With these sequences, the Im/Py pairings would be placed opposite C/G, A/T or T/A base pairs, and these results are similar to our results with f-ImPyIm suggesting that the f/Im behaves like a terminal Py/Im pairing <{[SECTION]}>(15)...
    • ...The heterocyclic content and, therefore, their cognate sequences are the main differences between these two triamides; however, f-ImPyIm recognizes CGCG with approximately one order of magnitude better affinity than mother nature recognizes AATT with distamycin A (15)...
    • ...The ‐ImPy‐ motif and its ‐GC‐ recognition site cannot be the only reason f-ImPyIm binds so tightly to CGCG because f-ImPyPy binds its cognate, AGCT, with approximately one-order of magnitude lower affinity (15)...

    Karen L. Buchmuelleret al. Molecular recognition of DNA base pairs by the formamido/pyrrole and f...

Sort by: