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Probing the folding pathways of four-stranded intercalated cytosine-rich motifs at single base-pair resolution
Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.ORCID iD: 0000-0001-6871-7663
Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.ORCID iD: 0000-0002-7815-4494
Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.ORCID iD: 0000-0002-4541-7702
2022 (English)In: Biochimie, ISSN 0300-9084, E-ISSN 1638-6183, Vol. 199, p. 81-91Article in journal (Refereed) Published
Abstract [en]

Cytosine-rich DNA can fold into four-stranded intercalated structures called i-motifs (iMs) under acidic conditions through the formation of hemi-protonated C:C+ base pairs. However, the folding and stability of iMs rely on many other factors that are not yet fully understood. Here, we combined biochemical and biophysical approaches to determine the factors influencing iM stability under a wide range of experimental conditions. By using high-resolution primer extension assays, circular dichroism, and absorption spectroscopies, we demonstrate that the stabilities of three different biologically relevant iMs are not dependent on molecular crowding agents. Instead, some of the crowding agents affected overall DNA synthesis. We also tested a range of small molecules to determine their effect on iM stabilization at physiological temperature and demonstrated that the G-quadruplex-specific molecule CX-5461 is also a promising candidate for selective iM stabilization. This work provides important insights into the requirements needed for different assays to accurately study iM stabilization, which will serve as important tools for understanding the contribution of iMs in cell regulation and their potential as therapeutic targets.

Place, publisher, year, edition, pages
Elsevier, 2022. Vol. 199, p. 81-91
Keywords [en]
CX-5461, DNA replication, G-quadruplex DNA, High-resolution primer extension assay, I-motif DNA, pH
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:umu:diva-194635DOI: 10.1016/j.biochi.2022.04.007ISI: 000800388200003PubMedID: 35452743Scopus ID: 2-s2.0-85129038456OAI: oai:DiVA.org:umu-194635DiVA, id: diva2:1657875
Funder
Swedish Research Council, 2021-02468Swedish Cancer Society, 2019/126Åke Wiberg Foundation, M20-0125Swedish Cancer Society, 21 0302 PT 01 HAvailable from: 2022-05-12 Created: 2022-05-12 Last updated: 2023-09-05Bibliographically approved

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Jamroskovic, JanDeiana, MarcoSabouri, Nasim

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