High-throughput single-molecule quantification of individual base stacking energies in nucleic acids
Abstract Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Ce...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-02-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-36373-8 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841559402236084224 |
|---|---|
| author | Jibin Abraham Punnoose Kevin J. Thomas Arun Richard Chandrasekaran Javier Vilcapoma Andrew Hayden Kacey Kilpatrick Sweta Vangaveti Alan Chen Thomas Banco Ken Halvorsen |
| author_facet | Jibin Abraham Punnoose Kevin J. Thomas Arun Richard Chandrasekaran Javier Vilcapoma Andrew Hayden Kacey Kilpatrick Sweta Vangaveti Alan Chen Thomas Banco Ken Halvorsen |
| author_sort | Jibin Abraham Punnoose |
| collection | DOAJ |
| description | Abstract Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Centrifuge Force Microscope for high-throughput single molecule experiments to measure stacking energies between adjacent bases. We found stacking energies strongest between purines (G|A at −2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at −0.5 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA nucleotides had no measurable effect, but a fluorophore modification reduced stacking energy. We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications. |
| format | Article |
| id | doaj-art-ef0ecd059a474bb888ca39c3aacfb9e0 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2023-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-ef0ecd059a474bb888ca39c3aacfb9e02025-01-05T12:34:30ZengNature PortfolioNature Communications2041-17232023-02-0114111310.1038/s41467-023-36373-8High-throughput single-molecule quantification of individual base stacking energies in nucleic acidsJibin Abraham Punnoose0Kevin J. Thomas1Arun Richard Chandrasekaran2Javier Vilcapoma3Andrew Hayden4Kacey Kilpatrick5Sweta Vangaveti6Alan Chen7Thomas Banco8Ken Halvorsen9The RNA Institute, University at Albany, State University of New YorkThe RNA Institute, University at Albany, State University of New YorkThe RNA Institute, University at Albany, State University of New YorkThe RNA Institute, University at Albany, State University of New YorkThe RNA Institute, University at Albany, State University of New YorkThe RNA Institute, University at Albany, State University of New YorkThe RNA Institute, University at Albany, State University of New YorkThe RNA Institute, University at Albany, State University of New YorkThe RNA Institute, University at Albany, State University of New YorkThe RNA Institute, University at Albany, State University of New YorkAbstract Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Centrifuge Force Microscope for high-throughput single molecule experiments to measure stacking energies between adjacent bases. We found stacking energies strongest between purines (G|A at −2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at −0.5 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA nucleotides had no measurable effect, but a fluorophore modification reduced stacking energy. We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications.https://doi.org/10.1038/s41467-023-36373-8 |
| spellingShingle | Jibin Abraham Punnoose Kevin J. Thomas Arun Richard Chandrasekaran Javier Vilcapoma Andrew Hayden Kacey Kilpatrick Sweta Vangaveti Alan Chen Thomas Banco Ken Halvorsen High-throughput single-molecule quantification of individual base stacking energies in nucleic acids Nature Communications |
| title | High-throughput single-molecule quantification of individual base stacking energies in nucleic acids |
| title_full | High-throughput single-molecule quantification of individual base stacking energies in nucleic acids |
| title_fullStr | High-throughput single-molecule quantification of individual base stacking energies in nucleic acids |
| title_full_unstemmed | High-throughput single-molecule quantification of individual base stacking energies in nucleic acids |
| title_short | High-throughput single-molecule quantification of individual base stacking energies in nucleic acids |
| title_sort | high throughput single molecule quantification of individual base stacking energies in nucleic acids |
| url | https://doi.org/10.1038/s41467-023-36373-8 |
| work_keys_str_mv | AT jibinabrahampunnoose highthroughputsinglemoleculequantificationofindividualbasestackingenergiesinnucleicacids AT kevinjthomas highthroughputsinglemoleculequantificationofindividualbasestackingenergiesinnucleicacids AT arunrichardchandrasekaran highthroughputsinglemoleculequantificationofindividualbasestackingenergiesinnucleicacids AT javiervilcapoma highthroughputsinglemoleculequantificationofindividualbasestackingenergiesinnucleicacids AT andrewhayden highthroughputsinglemoleculequantificationofindividualbasestackingenergiesinnucleicacids AT kaceykilpatrick highthroughputsinglemoleculequantificationofindividualbasestackingenergiesinnucleicacids AT swetavangaveti highthroughputsinglemoleculequantificationofindividualbasestackingenergiesinnucleicacids AT alanchen highthroughputsinglemoleculequantificationofindividualbasestackingenergiesinnucleicacids AT thomasbanco highthroughputsinglemoleculequantificationofindividualbasestackingenergiesinnucleicacids AT kenhalvorsen highthroughputsinglemoleculequantificationofindividualbasestackingenergiesinnucleicacids |