eprintid: 10205428 rev_number: 7 eprint_status: archive userid: 699 dir: disk0/10/20/54/28 datestamp: 2025-02-28 08:27:16 lastmod: 2025-02-28 08:27:16 status_changed: 2025-02-28 08:27:16 type: article metadata_visibility: show sword_depositor: 699 creators_name: Paul, Ananya creators_name: Terrell, J Ross creators_name: Farahat, Abdelbasset A creators_name: Ogbonna, Edwin N creators_name: Kumar, Arvind creators_name: Boykin, David W creators_name: Neidle, Stephen creators_name: Wilson, W David title: Alternative Approach to Sequence-Specific Recognition of DNA: Cooperative Stacking of Dication Dimers─Sensitivity to Compound Curvature, Aromatic Structure, and DNA Sequence ispublished: pub divisions: UCL divisions: B02 divisions: C08 divisions: D10 note: Copyright © 2025 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY 4.0, https://creativecommons.org/licenses/by/4.0/. abstract: With the growing number and diversity of known genome sequences, there is an increasing opportunity to regulate gene expression through synthetic, cell-permeable small molecules. Enhancing the DNA sequence recognition abilities of minor groove compounds has the potential to broaden their therapeutic applications with significant implications for areas such as modulating transcription factor activity. While various classes of minor groove binding agents can selectively identify pure AT and mixed AT and GC base pair(s) containing sequences, there remains a lack of compounds capable of distinguishing between different AT sequences. In this work, we report on the design compounds that exhibit selective binding to -TTAA- or -TATA- containing DNA minor groove sequences compared with other AT ones. Several studies have shown that the -AATT- and -TTAA- sequences have distinct physical and interaction properties, especially in terms of their different requirements for recognition in the minor groove. Achieving strong, selective minor groove binding at -TTAA- sequences has been challenging, but DB1003, a benzimidazole–furan–furan diamidine, has demonstrated cooperative dimeric binding activity at -TTAA-. It has significantly less binding preference for AATT. To better understand and modify the selectivity, we synthesized a set of rationally designed analogs of DB1003 by altering the position of the five-membered heterocyclic structure. Binding affinities and stoichiometries obtained from biosensor-surface plasmon resonance experiments show that DB1992, a benzimidazolefuran–thiophene diamidine, binds strongly to -TTAA- as a positive cooperative dimer with high cooperativity. The high-resolution crystal structure of the TTAA–DNA–DB1992 complex reveals that DB1992 binds as an antiparallel π-stacked dimer with numerous diverse contacts to the DNA minor groove. This distinctive binding arrangement and the properties of diamidines at the -TTAA- minor groove demonstrate that benzimidazole–furan–thiophene is a unique DNA binding pharmacophore. Competition mass spectroscopy and circular dichroism studies confirmed the binding stoichiometry and selectivity preference of the compounds for the -TTAA- sequence. date: 2025-02-21 date_type: published publisher: AMER CHEMICAL SOC official_url: https://doi.org/10.1021/acschembio.4c00800 oa_status: green full_text_type: pub language: eng primo: open primo_central: open_green verified: verified_manual elements_id: 2361725 doi: 10.1021/acschembio.4c00800 medium: Print-Electronic lyricists_name: Neidle, Stephen lyricists_id: SNEID18 actors_name: Harris, Jean actors_id: JAHAR68 actors_role: owner funding_acknowledgements: GM111749 [National Institutes of Health]; [National Institutes of Health]; DE-SC0012704 [DOE Office of Science]; [Brookhaven National Laboratory] full_text_status: public publication: ACS Chemical Biology volume: 20 number: 2 pagerange: 489-506 pages: 18 event_location: United States issn: 1554-8929 citation: Paul, Ananya; Terrell, J Ross; Farahat, Abdelbasset A; Ogbonna, Edwin N; Kumar, Arvind; Boykin, David W; Neidle, Stephen; Paul, Ananya; Terrell, J Ross; Farahat, Abdelbasset A; Ogbonna, Edwin N; Kumar, Arvind; Boykin, David W; Neidle, Stephen; Wilson, W David; - view fewer <#> (2025) Alternative Approach to Sequence-Specific Recognition of DNA: Cooperative Stacking of Dication Dimers─Sensitivity to Compound Curvature, Aromatic Structure, and DNA Sequence. ACS Chemical Biology , 20 (2) pp. 489-506. 10.1021/acschembio.4c00800 <https://doi.org/10.1021/acschembio.4c00800>. Green open access document_url: https://discovery.ucl.ac.uk/id/eprint/10205428/1/alternative_approach.pdf