Base pair mismatch has been regarded as the main source of DNA point mutations, where minor shortlived tautomers were usually involved. However, the detection and characterization of these unnatural species pose chall...Base pair mismatch has been regarded as the main source of DNA point mutations, where minor shortlived tautomers were usually involved. However, the detection and characterization of these unnatural species pose challenges to existing techniques. Here, by using systematic structural and ultrafast resonance Raman(RR) spectral analysis for the four possible conformers of guanine-cytosine base pairs, the prominent marker Raman bands were identified. We found that the hydrogen bonding vibrational region from 2300 cm^(-1) to 3700 cm^(-1) is ideal for the identification of these short live species. The marker bands provide direct evidence for the existence of the tautomer species, thus offering an effective strategy to detect the short-lived minor species. Ultrafast resonance Raman spectroscopy would be a powerful tool to provide direct evidence of critical dynamical details of complex systems involving protonation or tautomerization.展开更多
Cereal genes are classified into two distinct classes according to the guanine-cytosine （GC） content at the third codon sites （GC3）. Natural selection and mutation bias have been proposed to affect the GC content....Cereal genes are classified into two distinct classes according to the guanine-cytosine （GC） content at the third codon sites （GC3）. Natural selection and mutation bias have been proposed to affect the GC content. However, there has been controversy about the cause of GC variation. Here, we characterized the GC content of 1 092 paralogs and other single-copy genes in the duplicated chromosomal regions of the rice genome （ssp. indica） and classified the paralogs into GC3-rich and GC3-poor groups. By referring to out-group sequences from Arabidopsis and maize, we confirmed that the average synonymous substitution rate of the GC3-rich genes is significantly lower than that of the GC3-poor genes. Furthermore, we explored the other possible factors corresponding to the GC variation including the length of coding sequences, the number of exons in each gene, the number of genes in each family, the location of genes on chromosomes and the protein functions. Consequently, we propose that natural selection rather than mutation bias was the primary cause of the GC variation.展开更多
基金the financial support from the National Key Research and Development Program of China(No.2019YFA0708703)the National Natural Science Foundation of China(NSFC,No.21773309)+3 种基金the High-level Science Foundation of Qingdao Agricultural University(No.663/1114351)the Hefei National Laboratory for Physical Sciences at the Microscale(No.KF2020004)Xiangyang Science and Technology Research and Development(No.2020YL09)Hubei University of Arts and Science(Nos.HLOM222003,2020kypytd002)。
文摘Base pair mismatch has been regarded as the main source of DNA point mutations, where minor shortlived tautomers were usually involved. However, the detection and characterization of these unnatural species pose challenges to existing techniques. Here, by using systematic structural and ultrafast resonance Raman(RR) spectral analysis for the four possible conformers of guanine-cytosine base pairs, the prominent marker Raman bands were identified. We found that the hydrogen bonding vibrational region from 2300 cm^(-1) to 3700 cm^(-1) is ideal for the identification of these short live species. The marker bands provide direct evidence for the existence of the tautomer species, thus offering an effective strategy to detect the short-lived minor species. Ultrafast resonance Raman spectroscopy would be a powerful tool to provide direct evidence of critical dynamical details of complex systems involving protonation or tautomerization.
基金the State Key Basic Research and Development Plan of China(2003CB715900)the National Natural Science Foundation of China(90408015,30121003 and 30430030).
文摘Cereal genes are classified into two distinct classes according to the guanine-cytosine （GC） content at the third codon sites （GC3）. Natural selection and mutation bias have been proposed to affect the GC content. However, there has been controversy about the cause of GC variation. Here, we characterized the GC content of 1 092 paralogs and other single-copy genes in the duplicated chromosomal regions of the rice genome （ssp. indica） and classified the paralogs into GC3-rich and GC3-poor groups. By referring to out-group sequences from Arabidopsis and maize, we confirmed that the average synonymous substitution rate of the GC3-rich genes is significantly lower than that of the GC3-poor genes. Furthermore, we explored the other possible factors corresponding to the GC variation including the length of coding sequences, the number of exons in each gene, the number of genes in each family, the location of genes on chromosomes and the protein functions. Consequently, we propose that natural selection rather than mutation bias was the primary cause of the GC variation.
