Resolving altered base-pairing of RNA modifications with DNA nanoswitches
© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research..
There are >170 naturally occurring RNA chemical modifications, with both known and unknown biological functions. Analytical methods for detecting chemical modifications and for analyzing their effects are relatively limited and have had difficulty keeping pace with the demand for RNA chemical biology and biochemistry research. Some modifications can affect the ability of RNA to hybridize with its complementary sequence or change the selectivity of base pairing. Here, we investigate the use of affinity-based DNA nanoswitches to resolve energetic differences in hybridization. We found that a single m3C modification can sufficiently destabilize hybridization to abolish a detection signal, while an s4U modification can selectively hybridize with G over A. These results establish proof of concept for using DNA nanoswitches to detect certain RNA modifications and analyzing their effects in base pairing stability and specificity.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:51 |
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| Enthalten in: |
Nucleic acids research - 51(2023), 20 vom: 10. Nov., Seite 11291-11297 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Todkari, Iranna Annappa [VerfasserIn] |
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| Links: |
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| Themen: |
63231-63-0 |
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| Anmerkungen: |
Date Completed 15.11.2023 Date Revised 23.04.2024 published: Print Citation Status MEDLINE |
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| doi: |
10.1093/nar/gkad802 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 520 | |a © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. | ||
| 520 | |a There are >170 naturally occurring RNA chemical modifications, with both known and unknown biological functions. Analytical methods for detecting chemical modifications and for analyzing their effects are relatively limited and have had difficulty keeping pace with the demand for RNA chemical biology and biochemistry research. Some modifications can affect the ability of RNA to hybridize with its complementary sequence or change the selectivity of base pairing. Here, we investigate the use of affinity-based DNA nanoswitches to resolve energetic differences in hybridization. We found that a single m3C modification can sufficiently destabilize hybridization to abolish a detection signal, while an s4U modification can selectively hybridize with G over A. These results establish proof of concept for using DNA nanoswitches to detect certain RNA modifications and analyzing their effects in base pairing stability and specificity | ||
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| 700 | 1 | |a Punnoose, Jibin Abraham |e verfasserin |4 aut | |
| 700 | 1 | |a Mao, Song |e verfasserin |4 aut | |
| 700 | 1 | |a Haruehanroengra, Phensinee |e verfasserin |4 aut | |
| 700 | 1 | |a Beckles, Camryn |e verfasserin |4 aut | |
| 700 | 1 | |a Sheng, Jia |e verfasserin |4 aut | |
| 700 | 1 | |a Halvorsen, Ken |e verfasserin |4 aut | |
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