Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency
Abstract
:1. Introduction
2. Materials and Methods
2.1. Generation of Long-Adapter Single-Stranded Oligonucleotide Probe & Target Cloning
2.2. LASSO Capture Quantification for Single-Target and Library Experiments
2.3. Probe–Target Interaction Simulation
2.3.1. Order Parameter
2.3.2. Umbrella Sampling
2.3.3. Box Size and Salt Concentration
2.3.4. Procedure of Simulation
3. Results
3.1. Adapter Length-Dependent LASSO Probe Efficiency
3.2. The Effect of Secondary Structure Formed by LASSO
3.3. Calculation of Free Energy of Probe–Target Interaction
3.4. Comparison with Experiments
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Liu, J.; Shukor, S.; Li, S.; Tamayo, A.; Tosi, L.; Larman, B.; Nanda, V.; Olson, W.K.; Parekkadan, B. Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency. Biomolecules 2019, 9, 199. https://doi.org/10.3390/biom9050199
Liu J, Shukor S, Li S, Tamayo A, Tosi L, Larman B, Nanda V, Olson WK, Parekkadan B. Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency. Biomolecules. 2019; 9(5):199. https://doi.org/10.3390/biom9050199
Chicago/Turabian StyleLiu, Jingqian, Syukri Shukor, Shuxiang Li, Alfred Tamayo, Lorenzo Tosi, Benjamin Larman, Vikas Nanda, Wilma K. Olson, and Biju Parekkadan. 2019. "Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency" Biomolecules 9, no. 5: 199. https://doi.org/10.3390/biom9050199
APA StyleLiu, J., Shukor, S., Li, S., Tamayo, A., Tosi, L., Larman, B., Nanda, V., Olson, W. K., & Parekkadan, B. (2019). Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency. Biomolecules, 9(5), 199. https://doi.org/10.3390/biom9050199