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Short-interspersed nuclear elements are transcribed by RNA polymerase III which is known to transcribe ribosomal RNA and tRNA, two types of RNA vital to ribosomal assembly and mRNA translation. [8] SINEs, like tRNAs and many small-nuclear RNAs possess an internal promoter and thus are transcribed differently than most protein-coding genes. [ 1 ]
In order to create, i.e., design, RNA for any given secondary structure, two or three bases would not be enough, but four bases are enough. [16] This is likely why nature has "chosen" a four base alphabet: fewer than four would not allow the creation of all structures, while more than four bases are not necessary to do so.
Nucleic acid NMR is the use of nuclear magnetic resonance spectroscopy to obtain information about the structure and dynamics of nucleic acid molecules, such as DNA or RNA.It is useful for molecules of up to 100 nucleotides, and as of 2003, nearly half of all known RNA structures had been determined by NMR spectroscopy.
Double-stranded RNA forms an A-type helical structure, unlike the common B-type conformation taken by double-stranded DNA molecules. The secondary structure of RNA consists of a single polynucleotide. Base pairing in RNA occurs when RNA folds between complementarity regions. Both single- and double-stranded regions are often found in RNA molecules.
Two important functions are the binding potential with ligands or proteins, and its ability to stabilize the whole tertiary structure of DNA or RNA. The strong structure can inhibit or modulate transcription and replication, such as in the telomeres of chromosomes and the UTR of mRNA. [18] The base identity is important towards ligand binding.
This may be because 10% of genes in zebrafish have alternating TG and AC base pairs at the 3' splice site (3'ss) and 5' splice site (5'ss) respectively on each intron, which alters the secondary structure of the RNA. This suggests that secondary structure of RNA can influence splicing, potentially without the use of proteins like U2AF2 that ...
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