Complete Analysis on the Two Base Pair Sequence Recognition by Hx (pAnisylbenzimidazole)•Pyrrole and Hx•Imidazole Pairings

Student Author(s)

Samuel Tzou

Faculty Mentor(s)

Dr. Vijay Satam; Dr. Kimberly Brien; Dr. Pravin Patil; Dr. Balaji Babu; Dr. Moses Lee

Document Type


Event Date



Pyrrole (Py) and Imidazole (Im) polyamide analogs of distamycin are small molecules that bind in the minor groove at specific sequences of DNA and regulate gene function. Despite their potential in drug discovery or as tools in molecular and cell biology, their usefulness is limited by their ability to enter cells and concentrate in the nucleus. There is thus an effort to develop polyamides that are trackable in cells. Thus there is an immediate need for the design of novel heterocyclic DNA sequence cognitive units that exhibit all the positive qualities as Py and Im, and be inherently fluorescent. Our group has recently published a novel class of hybrid Hx-amides, which contain a fluorescent p-anisylbenzimidazole or Hx group. Pairing of Hx with PI, PP and IP provided evidence that it mimics “PyPy” in recognizing two contiguous base pairs in a similar way as polyamides. To complete our examination of the Hx functionality, the remaining molecule in this series, HxII, was successfully synthesized. The DNA binding properties of HxII will be reported along with a discussion on sequence recognition by Hx/polyamide pairings and gene control.

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