Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins
Abstract DNA-nanoparticle motor is a burnt-bridge Brownian ratchet moving on RNA-modified surface driven by Ribonuclease H (RNase H), and one of the fastest nanoscale artificial motors. However, its speed is still much lower than those of motor proteins. Here we resolve elementary processes of motio...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-56036-0 |
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| author | Takanori Harashima Akihiro Otomo Ryota Iino |
| author_facet | Takanori Harashima Akihiro Otomo Ryota Iino |
| author_sort | Takanori Harashima |
| collection | DOAJ |
| description | Abstract DNA-nanoparticle motor is a burnt-bridge Brownian ratchet moving on RNA-modified surface driven by Ribonuclease H (RNase H), and one of the fastest nanoscale artificial motors. However, its speed is still much lower than those of motor proteins. Here we resolve elementary processes of motion and reveal long pauses caused by slow RNase H binding are the bottleneck. As RNase H concentration ([RNase H]) increases, pause lengths shorten from ~70 s to ~0.2 s, while step sizes (displacements between two consecutive pauses) are constant ( ~ 20 nm). At high [RNase H], speed reaches ~100 nm s−1, however, processivity (total number of steps before detachment), run-length, and unidirectionality largely decrease. A geometry-based kinetic simulation reveals switching of bottleneck from RNase H binding to DNA/RNA hybridization at high [RNase H], and trade-off mechanism between speed and other performances. An engineered motor with 3.8-times larger DNA/RNA hybridization rate simultaneously achieves 30 nm s−1 speed, 200 processivity, and 3 μm run-length comparable to motor proteins. |
| format | Article |
| id | doaj-art-0941141205044f91828ceb5eb9aa4d9f |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-0941141205044f91828ceb5eb9aa4d9f2025-01-19T12:30:19ZengNature PortfolioNature Communications2041-17232025-01-0116111710.1038/s41467-025-56036-0Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteinsTakanori Harashima0Akihiro Otomo1Ryota Iino2Institute for Molecular Science, National Institutes of Natural SciencesInstitute for Molecular Science, National Institutes of Natural SciencesInstitute for Molecular Science, National Institutes of Natural SciencesAbstract DNA-nanoparticle motor is a burnt-bridge Brownian ratchet moving on RNA-modified surface driven by Ribonuclease H (RNase H), and one of the fastest nanoscale artificial motors. However, its speed is still much lower than those of motor proteins. Here we resolve elementary processes of motion and reveal long pauses caused by slow RNase H binding are the bottleneck. As RNase H concentration ([RNase H]) increases, pause lengths shorten from ~70 s to ~0.2 s, while step sizes (displacements between two consecutive pauses) are constant ( ~ 20 nm). At high [RNase H], speed reaches ~100 nm s−1, however, processivity (total number of steps before detachment), run-length, and unidirectionality largely decrease. A geometry-based kinetic simulation reveals switching of bottleneck from RNase H binding to DNA/RNA hybridization at high [RNase H], and trade-off mechanism between speed and other performances. An engineered motor with 3.8-times larger DNA/RNA hybridization rate simultaneously achieves 30 nm s−1 speed, 200 processivity, and 3 μm run-length comparable to motor proteins.https://doi.org/10.1038/s41467-025-56036-0 |
| spellingShingle | Takanori Harashima Akihiro Otomo Ryota Iino Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins Nature Communications |
| title | Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins |
| title_full | Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins |
| title_fullStr | Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins |
| title_full_unstemmed | Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins |
| title_short | Rational engineering of DNA-nanoparticle motor with high speed and processivity comparable to motor proteins |
| title_sort | rational engineering of dna nanoparticle motor with high speed and processivity comparable to motor proteins |
| url | https://doi.org/10.1038/s41467-025-56036-0 |
| work_keys_str_mv | AT takanoriharashima rationalengineeringofdnananoparticlemotorwithhighspeedandprocessivitycomparabletomotorproteins AT akihirootomo rationalengineeringofdnananoparticlemotorwithhighspeedandprocessivitycomparabletomotorproteins AT ryotaiino rationalengineeringofdnananoparticlemotorwithhighspeedandprocessivitycomparabletomotorproteins |