The structure of phenylalanine transfer ribonucleic acid(tRNA Phe ) in solution was explored by 1 H NMR spectroscopy to evaluate the effect of lanthanide ion on the structural and conformational change. It w...The structure of phenylalanine transfer ribonucleic acid(tRNA Phe ) in solution was explored by 1 H NMR spectroscopy to evaluate the effect of lanthanide ion on the structural and conformational change. It was found that La 3+ ions possess specific effects on the imino proton region of the 1 H NMR spectra for yeast tRNA Phe . The dependence of the imino proton spectra of yeast tRNA Phe as a function of La 3+ concentration was examined, and the results suggest that the tertiary base pair G 15 ·C 48 , which is located in the terminal in the augmented dihydrouridine helix(D helix), was markedly affected by La 3+ (shifted to downfield by as much as 0 35). Base pair U 8·A 14 in yeast tRNA Phe , which are stacked on G 15 ·C 48 , was also affected by added La 3+ when 1～2 Mg 2+ were also present. Another imino proton that may be affected by La 3+ in yeast tRNA Phe is that of the tertiary base pair G 19 ·C 56 . The assignment of this resonance in yeast tRNA Phe is tentative since it is located in the region of highly overlapping resonances beween 12 6 and 12 2. This base pair helps to anchor the D loop to the TΨC loop. The binding of La 3+ caused conformational change of tRNA, which is responsible for shifts to upfield or downfield in 1 H NMR spectra.展开更多
The effect of lanthanum ions on the structural and conformational change of yeast tRNA Phe was studied by 1H NMR. The results suggest that the tertiary base pair (G-15)(C-48), which was located in the terminal in the ...The effect of lanthanum ions on the structural and conformational change of yeast tRNA Phe was studied by 1H NMR. The results suggest that the tertiary base pair (G-15)(C-48), which was located in the terminal in the augmented dihydrouridine helix (D-helix), was markedly affected by adding La 3+ and shifted 0.33 downfield. Based pair (U-8)(A-14), which is associated with a tertiary interaction, links the base of the acceptor stem to the D-stem and anchors the elbow of the L structure, shifted 0.20 upfield. Another imino proton that may be affected by La 3+ in tRNA Phe is the tertiary base pair (G-19)(C-56). The assignment of this resonance is tentative since it is located in the region of highly overlapping resonances between 12.6 and 12.2. This base pair helps to anchor the D-loop to the TΨC loop.展开更多
A network of 3719 tRNA gene sequences was constructed using simplest alignment. Its topology, degree distribution and clustering coefficient were studied. The behaviors of the network shift from fluctuated distributio...A network of 3719 tRNA gene sequences was constructed using simplest alignment. Its topology, degree distribution and clustering coefficient were studied. The behaviors of the network shift from fluctuated distribution to scale-free distribution when the similarity degree of the tRNA gene sequences increases. The tRNA gene sequences with the same anticodon identity are more self-organized than those with different anticodon identities and form local clusters in the network. Some vertices of the local cluster have a high connection with other local clusters, and the probable reason was given. Moreover, a network constructed by the same number of random tRNA sequences was used to make comparisons. The relationships between the properties of the tRNA similarity network and the characters of tRNA evolutionary history were discussed.展开更多
文摘The structure of phenylalanine transfer ribonucleic acid(tRNA Phe ) in solution was explored by 1 H NMR spectroscopy to evaluate the effect of lanthanide ion on the structural and conformational change. It was found that La 3+ ions possess specific effects on the imino proton region of the 1 H NMR spectra for yeast tRNA Phe . The dependence of the imino proton spectra of yeast tRNA Phe as a function of La 3+ concentration was examined, and the results suggest that the tertiary base pair G 15 ·C 48 , which is located in the terminal in the augmented dihydrouridine helix(D helix), was markedly affected by La 3+ (shifted to downfield by as much as 0 35). Base pair U 8·A 14 in yeast tRNA Phe , which are stacked on G 15 ·C 48 , was also affected by added La 3+ when 1～2 Mg 2+ were also present. Another imino proton that may be affected by La 3+ in yeast tRNA Phe is that of the tertiary base pair G 19 ·C 56 . The assignment of this resonance in yeast tRNA Phe is tentative since it is located in the region of highly overlapping resonances beween 12 6 and 12 2. This base pair helps to anchor the D loop to the TΨC loop. The binding of La 3+ caused conformational change of tRNA, which is responsible for shifts to upfield or downfield in 1 H NMR spectra.
文摘The effect of lanthanum ions on the structural and conformational change of yeast tRNA Phe was studied by 1H NMR. The results suggest that the tertiary base pair (G-15)(C-48), which was located in the terminal in the augmented dihydrouridine helix (D-helix), was markedly affected by adding La 3+ and shifted 0.33 downfield. Based pair (U-8)(A-14), which is associated with a tertiary interaction, links the base of the acceptor stem to the D-stem and anchors the elbow of the L structure, shifted 0.20 upfield. Another imino proton that may be affected by La 3+ in tRNA Phe is the tertiary base pair (G-19)(C-56). The assignment of this resonance is tentative since it is located in the region of highly overlapping resonances between 12.6 and 12.2. This base pair helps to anchor the D-loop to the TΨC loop.
基金the National Natural Science Foundation of China (Nos. 10105007, 10334020, 90103035,10574088)
文摘A network of 3719 tRNA gene sequences was constructed using simplest alignment. Its topology, degree distribution and clustering coefficient were studied. The behaviors of the network shift from fluctuated distribution to scale-free distribution when the similarity degree of the tRNA gene sequences increases. The tRNA gene sequences with the same anticodon identity are more self-organized than those with different anticodon identities and form local clusters in the network. Some vertices of the local cluster have a high connection with other local clusters, and the probable reason was given. Moreover, a network constructed by the same number of random tRNA sequences was used to make comparisons. The relationships between the properties of the tRNA similarity network and the characters of tRNA evolutionary history were discussed.
