Literature DB >> 13129584

Comprehensive high-resolution analysis of hairpin polyamides utilizing a fluorescent intercalator displacement (FID) assay.

Winston C Tse1, Takahiro Ishii, Dale L Boger.   

Abstract

Four hairpin polyamides bearing subtle N- and C-terminal substitutions were examined in a fluorescent intercalator displacement (FID) assay enlisting a library of 512 DNA hairpins that contain all possible five base pair sequences in a challenging probe of its capabilities for establishing DNA binding sequence selectivity. Not only did the assay define the global sequence selectivity expected based on known structural interactions and Dervan's pairing rules establishing the utility of the method for characterizing such polyamides, but previously unappreciated subtle substituent effects on global sequence selectivity were also revealed. Thus, we report the discovery of a novel five base pair high affinity binding site of the form 5'-WWCWW (vs 5'-WGWWW) for the polyamide ImPyPy-gamma-PyPyPy-beta-Dp and its structural basis.

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Year:  2003        PMID： 13129584     DOI： 10.1016/s0968-0896(03)00455-3

Source DB:  PubMed          Journal:  Bioorg Med Chem        ISSN： 0968-0896            Impact factor:   3.641


  7 in total

1.  Defining the sequence-recognition profile of DNA-binding molecules.

Authors:  Christopher L Warren; Natasha C S Kratochvil; Karl E Hauschild; Shane Foister; Mary L Brezinski; Peter B Dervan; George N Phillips; Aseem Z Ansari
Journal:  Proc Natl Acad Sci U S A       Date:  2006-01-17       Impact factor: 11.205

2.  Discovery of inhibitors of aberrant gene transcription from Libraries of DNA binding molecules: inhibition of LEF-1-mediated gene transcription and oncogenic transformation.

Authors:  James S Stover; Jin Shi; Wei Jin; Peter K Vogt; Dale L Boger
Journal:  J Am Chem Soc       Date:  2009-03-11       Impact factor: 15.419

3.  Specificity landscapes of DNA binding molecules elucidate biological function.

Authors:  Clayton D Carlson; Christopher L Warren; Karl E Hauschild; Mary S Ozers; Naveeda Qadir; Devesh Bhimsaria; Youngsook Lee; Franco Cerrina; Aseem Z Ansari
Journal:  Proc Natl Acad Sci U S A       Date:  2010-02-22       Impact factor: 11.205

Review 4.  Inverse Electron Demand Diels-Alder Reactions of Heterocyclic Azadienes, 1-Aza-1,3-Butadienes, Cyclopropenone Ketals, and Related Systems. A Retrospective.

Authors:  Jiajun Zhang; Vyom Shukla; Dale L Boger
Journal:  J Org Chem       Date:  2019-05-23       Impact factor: 4.354

5.  CSI-FID: high throughput label-free detection of DNA binding molecules.

Authors:  Karl E Hauschild; James S Stover; Dale L Boger; Aseem Z Ansari
Journal:  Bioorg Med Chem Lett       Date:  2009-05-03       Impact factor: 2.823

6.  A fundamental relationship between hydrophobic properties and biological activity for the duocarmycin class of DNA-alkylating antitumor drugs: hydrophobic-binding-driven bonding.

Authors:  Amanda L Wolfe; Katharine K Duncan; James P Lajiness; Kaicheng Zhu; Adam S Duerfeldt; Dale L Boger
Journal:  J Med Chem       Date:  2013-08-29       Impact factor: 7.446

7.  Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing.

Authors:  Jordan L Meier; Abigail S Yu; Ian Korf; David J Segal; Peter B Dervan
Journal:  J Am Chem Soc       Date:  2012-10-10       Impact factor: 15.419
  7 in total

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