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Figure 2.20 Structure of RNA molecules. (A) Yeast tRNA. The base sequence is described as clover shaped. The thin lines depict the tertiary interactions between the base pairs. The bases circled in solid lines are those that are conserved in all tRNAs. Those bases circled in dotted lines are only semiconserved.

      Source: Voet et al. (2002). Reproduced with permission of John Wiley and Sons.

      (B) Secondary structure of 16S rRNA. a. Schematic representation, b. Structure of rRNA of the large ribomsome subunit of bacteria; colours of domains are identical to those in B.a; c. front view.

      Source: Courtesy of V. Ramakrishan, MRC, Cambridge.

      (C) An example of 23S rRNA (from Haloarcula marismortui, a halophilic red Archaeon found in the Dead Sea) with six domains (Domain I‐VI). a. Schematoic view; bv. Tertiary structure with six domains.

      Source: Courtesy of Thomas Steitz and Peter Moore, Yale University.

      RNA interference(RNAi) describes a widely distributed phenomenon in which double‐stranded RNA molecules lead to the breakdown of complementary mRNA. In the cell there is a ribonuclease (so‐called Dicer), which can cleave the double‐stranded RNA into short, 21‐ to 23‐nucleotide siRNA(short interfering RNA) molecules. The siRNA assembles itself together with proteins and forms the RNA‐induced silencing complex(RISC), which binds to the mRNA that is complementary to siRNA (e.g. of viruses or transposons). By cleaving the mRNA, the associated gene activity is inhibited. SiRNA regulates gene expression and rearrangements, by switching off transposons.

      A further group of small noncoding RNA molecules are the miRNAs (micro‐RNAs). An endogenous single‐stranded RNA molecule is produced by RNA polymerase II, which is then trimmed to miRNA 21–23 nucleotides in length by Dicer. miRNAs have been found in plants and animals. miRNA binds and inactivates complementary mRNA molecules and seems to play a very important role in gene regulation, differentiation, and tissue development.

      The RNAi method is an important tool for basic research in order to examine the function of genes. By introducing double‐stranded siRNA through transfection or with the help of a particle gun, targeted inhibition of gene activity is possible. It is also possible to produce transgenic cells that produce siRNA themselves. siRNA is a further development of the antisense RNAs and plays an important role as a tool for cellular/molecular biology and developmental biology, in order to silence all the genes of an organism in a specific way. Biotechnologists are also working on developing these molecules as therapeutics.

      Also the CRISPR‐mediated immunity of bacteria against viral infections employs small noncoding RNAs (crRNAs), similar to miRNA and siRNAs. When bacteria become infected with a virus, they manage to integrate short viral sequences into their genomes. These viral sequences become the templates for crRNAs, which can detect a future viral pathogen. When crRNAs have detected a complementary viral RNA, the latter is degraded by CRISPR‐associated proteins (Cas). The CRISPR/Cas system has recently been developed into a powerful system for gene editing in plants and animals, which avoids the traditional problems of recombinant DNA.

Catalytically active RNA molecules are important in ribosomes and were supposedly present in early evolution. These RNAs were surrounded by a simple biological membrane. They contained the genetic information and were also responsible for structure formation and catalysis. In addition to other tasks, they carried out protein synthesis. It is assumed that there was a division of labor further in the course of evolution, so that DNA took over the storage of genetic information and proteins took over the role as catalysts and structure carriers. Today, RNA has important roles both as a messenger between DNA and protein, as well as a catalytic and regulatory molecule.

Ribozymes are short RNA molecules that recognize and specifically cleave their target RNA via shared base sequences (Figure 2.21). Through selection of new ribozymes, biotechnologists are attempting to develop new enzyme‐like catalysts or therapeutics that can switch off unwanted gene activity.