Charge transport in individual short base stacked single-stranded RNA molecules
Abstract Charge transport in biomolecules is crucial for many biological and technological applications, including biomolecular electronics devices and biosensors. RNA has become the focus of research because of its importance in biomedicine, but its charge transport properties are not well understo...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-46263-0 |
| _version_ | 1797559455279218688 |
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| author | Subrata Chandra Ajoke Williams Farkhad Maksudov Evgenii Kliuchnikov Keshani G. G. Pattiya Arachchillage Patrick Piscitelli Aderlyn Castillo Kenneth A. Marx Valeri Barsegov Juan M. Artes Vivancos |
| author_facet | Subrata Chandra Ajoke Williams Farkhad Maksudov Evgenii Kliuchnikov Keshani G. G. Pattiya Arachchillage Patrick Piscitelli Aderlyn Castillo Kenneth A. Marx Valeri Barsegov Juan M. Artes Vivancos |
| author_sort | Subrata Chandra |
| collection | DOAJ |
| description | Abstract Charge transport in biomolecules is crucial for many biological and technological applications, including biomolecular electronics devices and biosensors. RNA has become the focus of research because of its importance in biomedicine, but its charge transport properties are not well understood. Here, we use the Scanning Tunneling Microscopy-assisted molecular break junction method to measure the electrical conductance of particular 5-base and 10-base single-stranded (ss) RNA sequences capable of base stacking. These ssRNA sequences show single-molecule conductance values around $$10^{-3}G_0$$ 10 - 3 G 0 ( $$G_0= 2e^2/h$$ G 0 = 2 e 2 / h ), while equivalent-length ssDNAs result in featureless conductance histograms. Circular dichroism (CD) spectra and MD simulations reveal the existence of extended ssRNA conformations versus folded ssDNA conformations, consistent with their different electrical behaviors. Computational molecular modeling and Machine Learning-assisted interpretation of CD data helped us to disentangle the structural and electronic factors underlying CT, thus explaining the observed electrical behavior differences. RNA with a measurable conductance corresponds to sequences with overall extended base-stacking stabilized conformations characterized by lower HOMO energy levels delocalized over a base-stacking mediating CT pathway. In contrast, DNA and a control RNA sequence without significant base-stacking tend to form closed structures and thus are incapable of efficient CT. |
| first_indexed | 2024-03-10T17:45:41Z |
| format | Article |
| id | doaj.art-26e57603d2494221a2af034351b3aeef |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T17:45:41Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-26e57603d2494221a2af034351b3aeef2023-11-20T09:31:13ZengNature PortfolioScientific Reports2045-23222023-11-0113111310.1038/s41598-023-46263-0Charge transport in individual short base stacked single-stranded RNA moleculesSubrata Chandra0Ajoke Williams1Farkhad Maksudov2Evgenii Kliuchnikov3Keshani G. G. Pattiya Arachchillage4Patrick Piscitelli5Aderlyn Castillo6Kenneth A. Marx7Valeri Barsegov8Juan M. Artes Vivancos9Department of Chemistry, University of MassachusettsDepartment of Chemistry, University of MassachusettsDepartment of Chemistry, University of MassachusettsDepartment of Chemistry, University of MassachusettsDepartment of Chemistry, University of MassachusettsDepartment of Chemistry, University of MassachusettsDepartment of Chemistry, University of MassachusettsDepartment of Chemistry, University of MassachusettsDepartment of Chemistry, University of MassachusettsDepartment of Chemistry, University of MassachusettsAbstract Charge transport in biomolecules is crucial for many biological and technological applications, including biomolecular electronics devices and biosensors. RNA has become the focus of research because of its importance in biomedicine, but its charge transport properties are not well understood. Here, we use the Scanning Tunneling Microscopy-assisted molecular break junction method to measure the electrical conductance of particular 5-base and 10-base single-stranded (ss) RNA sequences capable of base stacking. These ssRNA sequences show single-molecule conductance values around $$10^{-3}G_0$$ 10 - 3 G 0 ( $$G_0= 2e^2/h$$ G 0 = 2 e 2 / h ), while equivalent-length ssDNAs result in featureless conductance histograms. Circular dichroism (CD) spectra and MD simulations reveal the existence of extended ssRNA conformations versus folded ssDNA conformations, consistent with their different electrical behaviors. Computational molecular modeling and Machine Learning-assisted interpretation of CD data helped us to disentangle the structural and electronic factors underlying CT, thus explaining the observed electrical behavior differences. RNA with a measurable conductance corresponds to sequences with overall extended base-stacking stabilized conformations characterized by lower HOMO energy levels delocalized over a base-stacking mediating CT pathway. In contrast, DNA and a control RNA sequence without significant base-stacking tend to form closed structures and thus are incapable of efficient CT.https://doi.org/10.1038/s41598-023-46263-0 |
| spellingShingle | Subrata Chandra Ajoke Williams Farkhad Maksudov Evgenii Kliuchnikov Keshani G. G. Pattiya Arachchillage Patrick Piscitelli Aderlyn Castillo Kenneth A. Marx Valeri Barsegov Juan M. Artes Vivancos Charge transport in individual short base stacked single-stranded RNA molecules Scientific Reports |
| title | Charge transport in individual short base stacked single-stranded RNA molecules |
| title_full | Charge transport in individual short base stacked single-stranded RNA molecules |
| title_fullStr | Charge transport in individual short base stacked single-stranded RNA molecules |
| title_full_unstemmed | Charge transport in individual short base stacked single-stranded RNA molecules |
| title_short | Charge transport in individual short base stacked single-stranded RNA molecules |
| title_sort | charge transport in individual short base stacked single stranded rna molecules |
| url | https://doi.org/10.1038/s41598-023-46263-0 |
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