G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)<sub>n</sub> and (GA)<sub>n</sub> Repeats
The recently introduced semi-orthogonal system of nucleic acid imaging offers a greatly improved method of identifying DNA sequences that are capable of adopting noncanonical structures. This paper uses our newly developed G-QINDER tool to identify specific repeat sequences that adopt unique structu...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-04-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/24/8/7565 |
| _version_ | 1797605036078923776 |
|---|---|
| author | Lukáš Trizna Branislav Osif Viktor Víglaský |
| author_facet | Lukáš Trizna Branislav Osif Viktor Víglaský |
| author_sort | Lukáš Trizna |
| collection | DOAJ |
| description | The recently introduced semi-orthogonal system of nucleic acid imaging offers a greatly improved method of identifying DNA sequences that are capable of adopting noncanonical structures. This paper uses our newly developed G-QINDER tool to identify specific repeat sequences that adopt unique structural motifs in DNA: TG and AG repeats. The structures were found to adopt a left-handed G-quadruplex form under extreme crowding conditions and a unique tetrahelical motif under certain other conditions. The tetrahelical structure likely consists of stacked AGAG-tetrads but, unlike G-quadruplexes, their stability does not appear to be dependent on the type of monovalent cation present. The occurrence of TG and AG repeats in genomes is not rare, and they are also found frequently in the regulatory regions of nucleic acids, so it is reasonable to assume that putative structural motifs, like other noncanonical forms, could play an important regulatory role in cells. This hypothesis is supported by the structural stability of the AGAG motif; its unfolding can occur even at physiological temperatures since the melting temperature is primarily dependent on the number of AG repeats in the sequence. |
| first_indexed | 2024-03-11T04:55:25Z |
| format | Article |
| id | doaj.art-b5448c95f1d94b0681dad7a9c9471b07 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T04:55:25Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-b5448c95f1d94b0681dad7a9c9471b072023-11-17T19:42:23ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-04-01248756510.3390/ijms24087565G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)<sub>n</sub> and (GA)<sub>n</sub> RepeatsLukáš Trizna0Branislav Osif1Viktor Víglaský2Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, Pavol Jozef Šafárik University, 04001 Košice, SlovakiaDepartment of Biochemistry, Institute of Chemistry, Faculty of Sciences, Pavol Jozef Šafárik University, 04001 Košice, SlovakiaDepartment of Biochemistry, Institute of Chemistry, Faculty of Sciences, Pavol Jozef Šafárik University, 04001 Košice, SlovakiaThe recently introduced semi-orthogonal system of nucleic acid imaging offers a greatly improved method of identifying DNA sequences that are capable of adopting noncanonical structures. This paper uses our newly developed G-QINDER tool to identify specific repeat sequences that adopt unique structural motifs in DNA: TG and AG repeats. The structures were found to adopt a left-handed G-quadruplex form under extreme crowding conditions and a unique tetrahelical motif under certain other conditions. The tetrahelical structure likely consists of stacked AGAG-tetrads but, unlike G-quadruplexes, their stability does not appear to be dependent on the type of monovalent cation present. The occurrence of TG and AG repeats in genomes is not rare, and they are also found frequently in the regulatory regions of nucleic acids, so it is reasonable to assume that putative structural motifs, like other noncanonical forms, could play an important regulatory role in cells. This hypothesis is supported by the structural stability of the AGAG motif; its unfolding can occur even at physiological temperatures since the melting temperature is primarily dependent on the number of AG repeats in the sequence.https://www.mdpi.com/1422-0067/24/8/7565G-QINDER toolG-quadruplexnoncanonical DNA structuretetrahelical motif |
| spellingShingle | Lukáš Trizna Branislav Osif Viktor Víglaský G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)<sub>n</sub> and (GA)<sub>n</sub> Repeats International Journal of Molecular Sciences G-QINDER tool G-quadruplex noncanonical DNA structure tetrahelical motif |
| title | G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)<sub>n</sub> and (GA)<sub>n</sub> Repeats |
| title_full | G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)<sub>n</sub> and (GA)<sub>n</sub> Repeats |
| title_fullStr | G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)<sub>n</sub> and (GA)<sub>n</sub> Repeats |
| title_full_unstemmed | G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)<sub>n</sub> and (GA)<sub>n</sub> Repeats |
| title_short | G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)<sub>n</sub> and (GA)<sub>n</sub> Repeats |
| title_sort | g qinder tool bioinformatically predicted formation of different four stranded dna motifs from gt sub n sub and ga sub n sub repeats |
| topic | G-QINDER tool G-quadruplex noncanonical DNA structure tetrahelical motif |
| url | https://www.mdpi.com/1422-0067/24/8/7565 |
| work_keys_str_mv | AT lukastrizna gqindertoolbioinformaticallypredictedformationofdifferentfourstrandeddnamotifsfromgtsubnsubandgasubnsubrepeats AT branislavosif gqindertoolbioinformaticallypredictedformationofdifferentfourstrandeddnamotifsfromgtsubnsubandgasubnsubrepeats AT viktorviglasky gqindertoolbioinformaticallypredictedformationofdifferentfourstrandeddnamotifsfromgtsubnsubandgasubnsubrepeats |