Читать книгу Snyder and Champness Molecular Genetics of Bacteria - Tina M. Henkin - Страница 138

Unlike DNA, RNA is usually single stranded. However, pairing between the bases in different regions of the molecule may cause it to fold up on itself to form doublestranded regions. Such double-stranded regions are called the secondary structure of the RNA. All RNAs, including mRNAs, probably have extensive secondary structure.

Figure 2.1 RNA precursors. (A) A ribonucleoside triphosphate (rNTP) (the form of NTP used as a precursor for RNA) contains a ribose sugar, a base, and three phosphates. (B) The four bases in RNA. (C) An RNA polynucleotide chain with the 5′ and 3′ ends shown in red.

Figure 2.2 shows an example of RNA secondary structure in which the sequence 5′-AUCGGCA-3′ has paired with the complementary sequence 5′-UGCUGAU-3′ somewhere else in the molecule. As in double-stranded DNA, the paired strands of RNA are antiparallel, i.e., pairing occurs only when the two sequences are complementary when read in opposite directions (5′ to 3′ and 3′ to 5′) and the double-stranded RNA forms a helix that is similar to a DNA-DNA helix, capped with a few unpaired residues called a loop; the helix plus the loop are sometimes called a hairpin. However, the pairing rules for double-stranded RNA are slightly different from the pairing rules for DNA. As in DNA, G pairs with C, and A pairs with U (which replaces T in RNA). In RNA, guanine can pair not only with cytosine, but also with uracil. Because these G-U “wobble” pairs do not share hydrogen bonds, as indicated in the figure, they contribute less substantially to the stability of the double-stranded RNA. Additional “non-Watson-Crick” pairings are also found in RNA; these often involve surfaces of the nucleoside other than the normal hydrogen-bonding edge.

Figure 2.2 Secondary structure in an RNA. (A) The RNA folds back on itself to form a helical element sometimes called a hairpin. The presence of a GU pair (in parentheses) does not disrupt the structure. (B) Different regions of the RNA can also pair with each other to form a pseudoknot (participating residues shown in red). In the example, the loop of the hairpin pairs with another region of the RNA.

Each base pair that forms in the RNA makes the secondary structure more stable. Consequently, the RNA generally folds so that the greatest number of continuous base pairs can form. The stability of a structure can be predicted by adding up the energy of all of the hydrogen bonds that contribute to the structure. By eye, it is often difficult to predict which regions of a long RNA will pair to give the most stable structure. Computer software (e.g., mfold [http://mfold.rna.albany.edu/?q=mfold]) is available that, given the sequence of bases (primary structure) of the RNA, can predict the most stable secondary structure; however, the structure of complex RNAs is difficult to predict computationally because of interrupted base-pairing and non-Watson-Crick interactions.