RNAs carry out diverse biological functions, partly because different conformations of the same RNA sequence can play different roles in cellular activities. To fully understand the biological functions of RNAs requir...RNAs carry out diverse biological functions, partly because different conformations of the same RNA sequence can play different roles in cellular activities. To fully understand the biological functions of RNAs requires a conceptual framework to investigate the folding kinetics of RNA molecules, instead of native structures alone. Over the past several decades, many experimental and theoretical methods have been developed to address RNA folding. The helix-based RNA folding theory is the one which uses helices as building blocks, to calculate folding kinetics of secondary structures with pseudoknots of long RNA in two different folding scenarios. Here, we will briefly review the helix-based RNA folding theory and its application in exploring regulation mechanisms of several riboswitches and self-cleavage activities of the hepatitis delta virus (HDV) ribozyme.展开更多
Gene mutations influence the folding kinetics of hepatitis delta virus （HDV） ribozyme. In this work, we study the effect of the double mutation on the folding kinetics of HDV ribozyme. By using the master equation m...Gene mutations influence the folding kinetics of hepatitis delta virus （HDV） ribozyme. In this work, we study the effect of the double mutation on the folding kinetics of HDV ribozyme. By using the master equation method combined with RNA folding free energy landscape, we predict the folding kinetics of C13A：G82U and A16U：U79A mutated HDV sequences. Their folding pathways are identified by recursively searching the states with high net flux-in（out） population starting from the native state. The results indicate that the folding kinetics of C 13A：G82U mutation sequence is bi-phasic, which is similar to the wild type （wtHDV） sequence. While the folding kinetics of A16U：U79A mutation sequence is mono-phasic, it quickly folds to the native state in 30 s. Thus, the folding kinetics of double mutated HDV ribozyme depends on the mutation sites.展开更多
基金Project supported by the Science Fund from the Key Laboratory of Hubei Province, China (Grant No. 201932003)the National Natural Science Foundation of China (Grant Nos. 1157324 and 31600592).
文摘RNAs carry out diverse biological functions, partly because different conformations of the same RNA sequence can play different roles in cellular activities. To fully understand the biological functions of RNAs requires a conceptual framework to investigate the folding kinetics of RNA molecules, instead of native structures alone. Over the past several decades, many experimental and theoretical methods have been developed to address RNA folding. The helix-based RNA folding theory is the one which uses helices as building blocks, to calculate folding kinetics of secondary structures with pseudoknots of long RNA in two different folding scenarios. Here, we will briefly review the helix-based RNA folding theory and its application in exploring regulation mechanisms of several riboswitches and self-cleavage activities of the hepatitis delta virus (HDV) ribozyme.
基金Supported by the National Natural Science Foundation of China(31270761)
文摘Gene mutations influence the folding kinetics of hepatitis delta virus （HDV） ribozyme. In this work, we study the effect of the double mutation on the folding kinetics of HDV ribozyme. By using the master equation method combined with RNA folding free energy landscape, we predict the folding kinetics of C13A：G82U and A16U：U79A mutated HDV sequences. Their folding pathways are identified by recursively searching the states with high net flux-in（out） population starting from the native state. The results indicate that the folding kinetics of C 13A：G82U mutation sequence is bi-phasic, which is similar to the wild type （wtHDV） sequence. While the folding kinetics of A16U：U79A mutation sequence is mono-phasic, it quickly folds to the native state in 30 s. Thus, the folding kinetics of double mutated HDV ribozyme depends on the mutation sites.
