Conformational Transitions of Double-Stranded DNA in Thin Films
Conformational transitions of double-stranded DNA in different environments have long been studied as vital parts of both in vitro and in vivo processes. In this study, utilizing Fourier transform infrared spectroscopy (FTIR), we provide detailed analysis of dynamics of A- to B-form transitions in D...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-03-01
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| Series: | Applied Sciences |
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| Online Access: | https://www.mdpi.com/2076-3417/11/5/2360 |
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| author | Kristina Serec Nikola Šegedin Maria Krajačić Sanja Dolanski Babić |
| author_facet | Kristina Serec Nikola Šegedin Maria Krajačić Sanja Dolanski Babić |
| author_sort | Kristina Serec |
| collection | DOAJ |
| description | Conformational transitions of double-stranded DNA in different environments have long been studied as vital parts of both in vitro and in vivo processes. In this study, utilizing Fourier transform infrared spectroscopy (FTIR), we provide detailed analysis of dynamics of A- to B-form transitions in DNA thin films of different hydrated states based on a statistical analysis of a substantial number of spectra and band shape analysis (peak fitting) in both the phosphate (1150–1000 cm<sup>−1</sup>) and sugar–phosphate (900–750 cm<sup>−1</sup>) region. Hydration of DNA thin films is systematically controlled by the time spent in the desiccator chamber (from 3 min to 40 min) allowing conformation and hydration signatures, in addition to variations due to ambient conditions, to be resolved in the spectra. Conformation transition from A-form to more ordered B-form is observed if sufficient time in the desiccator chamber is allowed and is confirmed by changes on the bands at ≈890, 860, 837, and 805 cm<sup>−1</sup>. Phosphate vibrations at ≈1230 cm<sup>−1</sup> and 1089 cm<sup>−1</sup>, and backbone vibrations at ≈1030 cm<sup>−1</sup> and 765 cm<sup>−1</sup> were found to be sensitive to changes in hydration rather than conformation. Additionally, we found that spectral variations caused by ambient conditions can be significantly reduced without inducing conformational changes, which serves as a good basis for quality assurance. |
| first_indexed | 2024-03-09T05:08:09Z |
| format | Article |
| id | doaj.art-7db149e44a4047cf8df09690c558f4a2 |
| institution | Directory Open Access Journal |
| issn | 2076-3417 |
| language | English |
| last_indexed | 2024-03-09T05:08:09Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Applied Sciences |
| spelling | doaj.art-7db149e44a4047cf8df09690c558f4a22023-12-03T12:52:28ZengMDPI AGApplied Sciences2076-34172021-03-01115236010.3390/app11052360Conformational Transitions of Double-Stranded DNA in Thin FilmsKristina Serec0Nikola Šegedin1Maria Krajačić2Sanja Dolanski Babić3Department of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, CroatiaDepartment of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, CroatiaDepartment of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, CroatiaDepartment of Physics and Biophysics, School of Medicine, University of Zagreb, 10000 Zagreb, CroatiaConformational transitions of double-stranded DNA in different environments have long been studied as vital parts of both in vitro and in vivo processes. In this study, utilizing Fourier transform infrared spectroscopy (FTIR), we provide detailed analysis of dynamics of A- to B-form transitions in DNA thin films of different hydrated states based on a statistical analysis of a substantial number of spectra and band shape analysis (peak fitting) in both the phosphate (1150–1000 cm<sup>−1</sup>) and sugar–phosphate (900–750 cm<sup>−1</sup>) region. Hydration of DNA thin films is systematically controlled by the time spent in the desiccator chamber (from 3 min to 40 min) allowing conformation and hydration signatures, in addition to variations due to ambient conditions, to be resolved in the spectra. Conformation transition from A-form to more ordered B-form is observed if sufficient time in the desiccator chamber is allowed and is confirmed by changes on the bands at ≈890, 860, 837, and 805 cm<sup>−1</sup>. Phosphate vibrations at ≈1230 cm<sup>−1</sup> and 1089 cm<sup>−1</sup>, and backbone vibrations at ≈1030 cm<sup>−1</sup> and 765 cm<sup>−1</sup> were found to be sensitive to changes in hydration rather than conformation. Additionally, we found that spectral variations caused by ambient conditions can be significantly reduced without inducing conformational changes, which serves as a good basis for quality assurance.https://www.mdpi.com/2076-3417/11/5/2360DNA thin filmsFTIRhydrationconformationpeak fittingA-form |
| spellingShingle | Kristina Serec Nikola Šegedin Maria Krajačić Sanja Dolanski Babić Conformational Transitions of Double-Stranded DNA in Thin Films Applied Sciences DNA thin films FTIR hydration conformation peak fitting A-form |
| title | Conformational Transitions of Double-Stranded DNA in Thin Films |
| title_full | Conformational Transitions of Double-Stranded DNA in Thin Films |
| title_fullStr | Conformational Transitions of Double-Stranded DNA in Thin Films |
| title_full_unstemmed | Conformational Transitions of Double-Stranded DNA in Thin Films |
| title_short | Conformational Transitions of Double-Stranded DNA in Thin Films |
| title_sort | conformational transitions of double stranded dna in thin films |
| topic | DNA thin films FTIR hydration conformation peak fitting A-form |
| url | https://www.mdpi.com/2076-3417/11/5/2360 |
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