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Sengupta, Pallabi
Publications (3 of 3) Show all publications
Bose, D., Banerjee, N., Roy, A., Sengupta, P. & Chatterjee, S. (2024). Switchable tetraplex elements in the heterogeneous nuclear ribonucleoprotein K promoter: micro-environment dictated structural transitions of G/C rich elements. Journal of Biomolecular Structure and Dynamics
Open this publication in new window or tab >>Switchable tetraplex elements in the heterogeneous nuclear ribonucleoprotein K promoter: micro-environment dictated structural transitions of G/C rich elements
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2024 (English)In: Journal of Biomolecular Structure and Dynamics, ISSN 0739-1102, E-ISSN 1538-0254Article in journal (Refereed) Epub ahead of print
Abstract [en]

We have elucidated the hnRNP K promoter as a hotspot for tetraplex-based molecular switches receptive to micro-environmental stimuli. We have characterised the structural features of four tetraplex-forming loci and identified them as binding sites of transcription factors. These segments form either G-quadruplex or i-motif structures, the structural dynamicity of which has been studied in depth via several biophysical techniques. The tetraplexes display high dynamicity and are influenced by both pH and KCl concentrations in vitro. The loci complementary to these sequences form additional non-canonical secondary structures. In the cellular context, the most eminent observation of this study is the binding of hnRNP K to the i-motif forming sequences in its own promoter. We are the first to report a probable transcriptional autoregulatory function of hnRNP K in coordination with higher-order DNA structures. Herein, we also report the positive interaction of the endogenous tetraplexes with Sp1, a well-known transcriptional regulator. Treatment with tetraplex-specific small molecule ligands further uncovered G-quadruplexes’ functioning as repressors and i-motifs as activators in this context. Together, our findings strongly indicate the critical regulatory role of the identified tetraplex elements in the hnRNP K promoter. Communicated by Ramaswamy H. Sarma.

Place, publisher, year, edition, pages
Taylor & Francis, 2024
Keywords
DNA polymorphism, G-quadruplex, hairpin, hnRNP K, i-motif
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-220013 (URN)10.1080/07391102.2024.2303378 (DOI)001144526300001 ()38235706 (PubMedID)2-s2.0-85182447143 (Scopus ID)
Available from: 2024-01-30 Created: 2024-01-30 Last updated: 2024-02-09
Sengupta, P., Jamroskovic, J. & Sabouri, N. (2023). A beginner's handbook to identify and characterize i-motif DNA. In: Kevin D. Raney; Robert L. Eoff; Alicia K. Byrd; Samantha Kendrick (Ed.), Methods in enzymology: G4 and i-motif biology (pp. 45-70). Elsevier
Open this publication in new window or tab >>A beginner's handbook to identify and characterize i-motif DNA
2023 (English)In: Methods in enzymology: G4 and i-motif biology / [ed] Kevin D. Raney; Robert L. Eoff; Alicia K. Byrd; Samantha Kendrick, Elsevier, 2023, p. 45-70Chapter in book (Refereed)
Abstract [en]

Genomic DNA exhibits an innate ability to manifest diverse sequence-dependent secondary structures, serving crucial functions in gene regulation and cellular equilibrium. While extensive research has confirmed the formation of G-quadruplex structures by guanine-rich sequences in vitro and in cells, recent investigations have turned the quadruplex community's attention to the cytosine (C)-rich complementary strands that can adopt unique tetra-stranded conformation, termed as intercalated motif or i-motif. I-motifs are stabilized by hemi-protonated C:CH+ base pairs under acidic conditions. Initially, the in vivo occurrence of i-motifs was underestimated because their formation is favored at non-physiological pH. However, groundbreaking research utilizing the structure-specific iMab antibody and high-throughput sequencing have recently detected their conserved dispersion throughout the genome, challenging previous assumptions. Given the evolving nature of this research field, it becomes imperative to conduct independent in vitro experiments aimed at identifying potential i-motif formation in C-rich sequences and consolidating the findings to address the properties of i-motifs. This chapter serves as an introductory guide for the swift identification of novel i-motifs, where we present an experimental framework for investigating and characterizing i-motif sequences in vitro. In this chapter, we selected a synthetic oligonucleotide (C7T3) sequence and outlined appropriate methodologies for annealing the i-motif structure into suitable buffers. Then, we validated its formation by CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance) spectroscopy. Finally, we provided a thorough account of the step-by-step procedures to investigate the effect of i-motif formation on the stalling or retardation of DNA replication using high resolution primer extension assays.

Place, publisher, year, edition, pages
Elsevier, 2023
Series
Methods in enzymology, ISSN 0076-6879 ; 695
Keywords
Circular dichroism, I-motifs, Nuclear magnetic resonance, Primer extension assay, Quadruplex DNA
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-218112 (URN)10.1016/bs.mie.2023.11.001 (DOI)38521590 (PubMedID)2-s2.0-85178602961 (Scopus ID)978-0-443-21774-6 (ISBN)
Funder
Swedish Cancer Society, 22 2380 Pj 01HSwedish Research Council, VR-MH 2021-02468Knut and Alice Wallenberg Foundation, KAW 2021.0173The Kempe Foundations, SMK2058Wenner-Gren Foundations, o.UPD2020-0097Åke Wiberg Foundation, M20-0125
Available from: 2023-12-19 Created: 2023-12-19 Last updated: 2024-07-01Bibliographically approved
Deiana, M., Andrés Castán, J. M., Josse, P., Kahsay, A., Sánchez, D. P., Morice, K., . . . Sabouri, N. (2023). A new G-quadruplex-specific photosensitizer inducing genome instability in cancer cells by triggering oxidative DNA damage and impeding replication fork progression. Nucleic Acids Research, 51(12), 6264-6285
Open this publication in new window or tab >>A new G-quadruplex-specific photosensitizer inducing genome instability in cancer cells by triggering oxidative DNA damage and impeding replication fork progression
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2023 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 51, no 12, p. 6264-6285Article in journal (Refereed) Published
Abstract [en]

Photodynamic therapy (PDT) ideally relies on the administration, selective accumulation and photoactivation of a photosensitizer (PS) into diseased tissues. In this context, we report a new heavy-atom-free fluorescent G-quadruplex (G4) DNA-binding PS, named DBI. We reveal by fluorescence microscopy that DBI preferentially localizes in intraluminal vesicles (ILVs), precursors of exosomes, which are key components of cancer cell proliferation. Moreover, purified exosomal DNA was recognized by a G4-specific antibody, thus highlighting the presence of such G4-forming sequences in the vesicles. Despite the absence of fluorescence signal from DBI in nuclei, light-irradiated DBI-treated cells generated reactive oxygen species (ROS), triggering a 3-fold increase of nuclear G4 foci, slowing fork progression and elevated levels of both DNA base damage, 8-oxoguanine, and double-stranded DNA breaks. Consequently, DBI was found to exert significant phototoxic effects (at nanomolar scale) toward cancer cell lines and tumor organoids. Furthermore, in vivo testing reveals that photoactivation of DBI induces not only G4 formation and DNA damage but also apoptosis in zebrafish, specifically in the area where DBI had accumulated. Collectively, this approach shows significant promise for image-guided PDT.

Place, publisher, year, edition, pages
Oxford University Press, 2023
National Category
Biochemistry and Molecular Biology Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-212227 (URN)10.1093/nar/gkad365 (DOI)000988008500001 ()37191066 (PubMedID)2-s2.0-85164253573 (Scopus ID)
Funder
Swedish Cancer Society, 22 2380 PjSwedish Research Council, VR-MH 2021–02468Knut and Alice Wallenberg Foundation, KAW 2021-0173Swedish Cancer Society, 21 0302 PT 01 HWenner-Gren Foundations, UPD2020-0097Swedish Cancer Society, 20 0827 PjFCancerforskningsfonden i Norrland, LP 22-2312Cancerforskningsfonden i Norrland, LP20 1024 2257Cancerforskningsfonden i Norrland, LP 21–2298Swedish Research Council, 2017-01531Swedish Society of Medicine, SLS-890521Region Västerbotten, RV-930167Sjöberg FoundationKnut and Alice Wallenberg Foundation, KAW 2015.0114Marianne and Marcus Wallenberg Foundation, MMW 2020.0189Swedish Cancer Society, 20 1339 PjF
Available from: 2023-07-21 Created: 2023-07-21 Last updated: 2024-07-02Bibliographically approved
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