Life on Minerals: Binding Behaviors of Oligonucleotides on Zirconium Silicate and Its Inhibitory Activity for the Self-Cleavage of Hammerhead Ribozyme
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials
2.2. Nucleic Acid Solutions Preparation
2.3. Self-Cleavage Behaviors of ASBVd(−):HHR on Minerals
2.4. HPLC Analysis for the Products of ASBVd(−):HHR Self-Cleavage
2.5. Secondary Structure Modeling of RNA and DNA
3. Results and Discussion
3.1. Concept of RNA Chemical Network Model on Mineral
3.2. Selection of Oligonucleotides and Minerals
3.3. Binding Behaviors of DNA
3.4. Binding Behaviors of Oligo(A)
3.5. Binding Behaviors of Ribozymes and Desorption by EDTA Solution
3.6. Self-Cleavage of ASBVd(−):HHR on Zirconium Silicate and Montmorillonite Surfaces
3.7. Role of Minerals for the Chemical Evolution of Ribozymes on Hadean Earth
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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# | RNA Name | Sequence |
---|---|---|
1 | ASBVd79(−):HHR | GGUUCUUCCC AUCUUUCCCU GAAGAGACGA AGCAAGUCGA AACUCAGAGU CGGAAAGUCG GAACAGACCU GGUUUCGUC |
2 | rna-ASBVd45 | CUUUCCCU GAAGAGACGA AGCAAGUCGA AACUCAGAGU CGGAAAG |
3 | rna-ASBVd45-3′(GA)5 | CUUUCCCU GAAGAGACGA AGCAAGUCGA AACUCAGAGU CGGAAAG GAGAGAGAGA |
4 | rna-ASBVd45-3′C10 | CUUUCCCU GAAGAGACGA AGCAAGUCGA AACUCAGAGU CGGAAAG CCCCCCCCCC |
5 | rna-ASBVd45-5′(GA)5 | GAGAGAGAGA CUUUCCCU GAAGAGACGA AGCAAGUCGA AACUCAGAGU CGGAAAG |
6 | rna-ASBVd45-5′C10 | CCCCCCCCCC CUUUCCCU GAAGAGACGA AGCAAGUCGA AACUCAGAGU CGGAAAG |
# | DNA Name | Sequence |
---|---|---|
1 | dna-ASBVd45 | CTTTCCCT GAAGAGACGA AGCAAGTCGA AACTCAGAGT CGGAAAG |
2 | dna-ASBVd45-5′(GA)5 | GAGAGAGAGA CTTTCCCT GAAGAGACGA AGCAAGTCGA AACTCAGAGT CGGAAAG |
3 | dna-ASBVd45-5′C10 | CCCCCCCCCC CTTTCCCT GAAGAGACGA AGCAAGTCGA AACTCAGAGT CGGAAAG |
4 | dna-ASBVd45-3′C10 | CTTTCCCT GAAGAGACGA AGCAAGTCGA AACTCAGAGT CGGAAAG CCCCCCCCCC |
5 | dna-ASBVd45-3′A10 | CTTTCCCT GAAGAGACGA AGCAAGTCGA AACTCAGAGT CGGAAAG AAAAAAAAAA |
6 | dna-ASBVd45-3′(GA)5 | CTTTCCCT GAAGAGACGA AGCAAGTCGA AACTCAGAGT CGGAAAG GAGAGAGAGA |
7 | dna-ASBVd45-3′(GA)10 | CTTTCCCT GAAGAGACGA AGCAAGTCGA AACTCAGAGT CGGAAAG GAGAGAGAGA GAGAGAGAGA |
8 | dna-ASBVd45-3′(GA)15 | CTTTCCCT GAAGAGACGA AGCAAGTCGA AACTCAGAGT CGGAAAG GAGAGAGAGA GAGAGAGAGA GAGAGAGAGA |
9 | dna-ASBVd45-3′(GA)20 | CTTTCCCT GAAGAGACGA AGCAAGTCGA AACTCAGAGT CGGAAAG GAGAGAGAGA GAGAGAGAGA GAGAGAGAGA GAGAGAGAGA |
10 | dna-ASBVd45-3′(GA)25 | CTTTCCCT GAAGAGACGA AGCAAGTCGA AACTCAGAGT CGGAAAG GAGAGAGAGA GAGAGAGAGA GAGAGAGAGA GAGAGAGAGA GAGAGAGAGA |
Minerals | Area (BET)/m2 g−1 |
---|---|
Aerosil | 3.69 × 102 |
Sepiolite | 3.51× 102 |
Zirconium silicate | 4.82 × 100 |
Montmorillonite | 2.29 × 102 |
Conditions | k/min−1 * |
---|---|
Control | (80.0 ± 11.0) × 10−4 |
In the presence of zirconium silicate | (2.46 ± 1.12) × 10−4 |
In the presence of montmorillonite | (2.38 ± 0.55) × 10−4 |
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Kawamura, K.; Lambert, J.-F.; Ter-Ovanessian, L.M.P.; Vergne, J.; Hervé, G.; Maurel, M.-C. Life on Minerals: Binding Behaviors of Oligonucleotides on Zirconium Silicate and Its Inhibitory Activity for the Self-Cleavage of Hammerhead Ribozyme. Life 2022, 12, 1689. https://doi.org/10.3390/life12111689
Kawamura K, Lambert J-F, Ter-Ovanessian LMP, Vergne J, Hervé G, Maurel M-C. Life on Minerals: Binding Behaviors of Oligonucleotides on Zirconium Silicate and Its Inhibitory Activity for the Self-Cleavage of Hammerhead Ribozyme. Life. 2022; 12(11):1689. https://doi.org/10.3390/life12111689
Chicago/Turabian StyleKawamura, Kunio, Jean-François Lambert, Louis M. P. Ter-Ovanessian, Jacques Vergne, Guy Hervé, and Marie-Christine Maurel. 2022. "Life on Minerals: Binding Behaviors of Oligonucleotides on Zirconium Silicate and Its Inhibitory Activity for the Self-Cleavage of Hammerhead Ribozyme" Life 12, no. 11: 1689. https://doi.org/10.3390/life12111689