Conditional cooperativity in DNA minor-groove recognition by oligopeptides

Lah, Jurij (author), Hadži, San (author)

The recognition of specific DNA sequences in processes such as transcription is associated with a cooperative binding of proteins. Some transcription regulation mechanisms involve additional proteins that can influence the binding cooperativity by acting as corepressors or coactivators. In a conditional cooperativity mechanism, the same protein can induce binding cooperativity at one concentration and inhibit it at another. Here, we use calorimetric (ITC) and spectroscopic (UV, CD) experiments to show that such conditional cooperativity can also be achieved by the small DNA-directed oligopeptides distamycin and netropsin. Using a global thermodynamic analysis of the observed binding and (un)folding processes, we calculate the phase diagrams for this system, which show that distamycin binding cooperativity is more pronounced at lower temperatures and can be first induced and then reduced by increasing the netropsin or/and Na+ ion concentration. A molecular interpretation of this phenomenon is suggested.

• Language: English
• Keywords: DNA recognition, conditional cooperativity, transcription regulation, protein–DNA interactions, ligand–DNA interactions, distamycin, netropsin, thermodynamics of binding, phase diagrams, DNA folding
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Publication status: Published
• Publication version: Version of Record
• Year: 2021
• Number of pages: 10 str.
• Numbering: Vol. 26, iss. 17, art. 5188
• PID: 20.500.12556/RUL-136078
• UDC: 577.323
• ISSN on article: 1420-3049
• DOI: 10.3390/molecules26175188
• COBISS.SI-ID: 87050755
• Publication date in RUL: 11.04.2022

Record is a part of a journal

• Title: Molecules
• Shortened title: Molecules
• Publisher: MDPI
• ISSN: 1420-3049
• COBISS.SI-ID: 18462981

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 01.09.2021

Secondary language

• Language: Slovenian
• Keywords: prepoznavanje DNA, pogojna kooperativnost, regulacija transkripcije, interakcije protein – DNA, interakcije ligand – DNA, distamicin, netropsin, termodinamika vezave, fazni diagrami, zvitje DNA

Projects

• Funder: ARRS - Slovenian Research Agency
• Project number: P1-0201
• Name: Fizikalna kemija

• Funder: ARRS - Slovenian Research Agency
• Project number: J1-1706
• Name: Stabilnost nove vrste kvadruplesov DNA (AGCGA) in njihovo prepoznavanje z nanotelesi