MD Simulations About The Folding Mechanism Of Nucleic Molecules

As proteins, nucleic acids are essential constituents of living organism. In the tra-ditional central dogma of molecular biology, DNA is the vehicle of genetic information, and storing the genetic information of living; in transcription process, RNA molecules are formed based on the template DNA; finally, proteins express from the RNA and supply the necessary constituents for living. As their is more understanding for the function of nucleic acids from the research, the central dogma of molecular biology become more and more complicated. For example, researches have show that RNA can transcript to DNA with the assistance of reverse transcriptase, and RNA can also transcript to RNA using itself as template. A point should be noted is the recently re-searches about non-coding RNA enrich our understanding of RNA vastly. Non-coding RNA a RNA molecule that functions without being translated into a protein. Small non-coding RNA is constituted by20-500nucleic acids, while long on-coding RNA is constituted by thousands to tens of thousands of nucleic acids. Although non-coding RNA can not translate to proteins, they still play important role in life process. The bi-ological functions of non-coding RNA include transcriptional regulation, chromosome replication, RNA processing and modification, messenger RNA stability and transla-tion, and even protein translocation. All these research show the import role of nucleic acids in the genetic variability, and the importance of further understanding of nucleic acids in more research. One of such research field is exploring the folding mechanism of nucleic acids. Nucleic acids also can form some stable structure when perform-ing their function. For example, the promoter must bind to some proteins to start the replication process of DNA. In this case, DNA can form some structure to assist this process. Telomere is a type of single strand DNA and lies at the end of chromosome, it can fold to special structure to protect the chromosome. When binding to proteins or performing other biological function, RNA also need to form some stable structures to play an assistance role. Studying the folding process of nucleic acids can help us further understanding their roles in physiological. On the other hand, the studying of folding mechanism of nucleic acids can verify the energy landscape theory which is applied in the field of protein folding.Molecular dynamics (MD) simulation is an optimal option when studying the folding mechanism of nucleic acids. It is an widely used method in Biophysics, Bio-chemistry and Solid state physics et al. to study complex systems. Depending on the principle of Newton force, MD simulation has the advantage of high accuracy, reflect-ing the information of the system in dynamics and statistical thermodynamics clearly, and supplementing the results from experiment. However, conventional MD simula-tion has some limitation. For example, when the studying system has some free energy local minima, such as the folding of protein, it will trap in the minima and it will cost much time to escape. So, the system will just sample the local ensemble in accepting time range and we can’t obtain the global information. Nowadays, people mainly solve such problem by developing sampling methods. Such methods includ coarse grained models (such as Go model), umbrella sampling, replica exchange molecular dynam-ics, Metadynamics and transition path sampling, et al. Although these methods have their own advantage, their accuracy applied in complex system still need to be further verified.As the importance of the research about the folding mechanism of nucleic acids and ensemble sampling methods, we carried out the following research.Firstly, using coarse grained model (Go model) to explore the ensemble of pro-tein ci2, we tested the accuracy of the Metadynamics method and its variants. From the simulation results, it indicates that the conventional Metadynamcis has high efficiency when sampling the conformational space and can give a coarse free energy landscape. The well-tempered Metadynamics can solve the problem of convergence in conven-tional Metadynamcis. If the parameters are chosen reasonably, from well-tempered Metadynamics, we can obtain more accurate results than conventional Metadynam-cis. Bias exchange Metadynamics method has the highest accuracy among the variant Metadynamics methods and the results from the unbiased replica has the most opti-mal results. Depending on our results, it is useful for people to apply Metadynamics reasonably and obtain much more accurate results.Based on the accuracy testing for Metadynamics and its variants, we applied Bias exchange Metadynamics to explore the folding mechanism of two nucleic acids sys-tem:DNA G-quadruplex and RNA pseudoknot.G-quadruplex is a structure formed by the sequence rich in guanine, which can usually be observed in telomere. Lies at the end of chromosome, telomere has lots of TTAGGG repeat and can play important role in keeping the integrity of chromo-some, protecting the chromosome not to be degraded and preventing the chromosome fusion. Furthermore, many researches have indicated that G-quadruplex in telomere can inhibit the activity of telomerase which can play important role in cancer cells. So, studying the property of telomeric G-quadruplex is benefit to develop anticancer medicine. In our second word, we combined Bias exchange Metadynamics and con-ventional MD simulations to explore the folding mechanism of G-quadruplex. Using the the Bias exchange Metadynamics, we computed the free energy landscape and ob-served for intermediates, including a G-triplex and a native-like state. Then, we applied conventional MD to study the stability and architectural feature of these intermediates. In addition, we also discussed the role of K+in the folding process. This work gives results agree with experimental ones and displayed an atomistic picture for the folding process.Pseudoknot is a common structure in RNA, including non-coding RNA, and it can play important role in transcription and expression of gene. For example, pse-doknot can help the same mRNA translate into different proteins by frame shifting mechanism. Furthermore, there are both secondary and tertiary structure, canonical and noncanonical base pairs and so on in RNA pseudoknot and these are hot problems people concerning about. So, pseudoknot is a good model to study the folding mecha-nism and other properties of RNA. In addition, the large flexibility of loop in psedoknot make it to be a big problem in RNA structure prediction. In our work, we applied Bias exchange Metadynamics to study the folding mechanism of mRNA within gene32of bacteriophage T2which is a pseudoknot structure. Depending on the ensemble sam-pling and the free energy analysis, we found multiple intermediates and the diversity of folding pathways. The conclusions of multiple folding pathways and the step by step formation of hairpin in our simulation is consistent to the experiment one. In this work, we also displayed the architectural feature of the intermediates and atomistic picture for the folding process.The contents of this thesis are arranged below. In the first chapter, we will in-troduce the Metadynamics method and its variants, architectural feature of DNA and RNA. The thermodynamics and kinetics of DNA and RNA will be also discussed. In the second chapter, we will introduce the work about testing the accuracy of Meta-dynamics and its variants. In the third chapter, we will introduce the work about the folding mechanism of DNA G-quadruplex by combining Bias exchange Metadynamics and conventional MD. In the fourth chapter, we will introduce the work about folding mechanism of RNA pseudoknot by using Bias exchange Metadynamics. Finally, in the fifth chaper, we will give conclusions about this thesis and give suggestion for further study.