Stem-loop structures

RNA decoys from HCV stem-loop structures in NS5B coding region sequester replication complexes HCV (Zhang et al. 2005)... 

Alternatively, one interesting drug delivery technique exploits the active transport of certain naturally-occurring and relatively small biomacromolecules across the cellular membrane. For instance, the nuclear transcription activator protein (Tat) from HIV type 1 (HlV-1) is a 101-amino acid protein that must interact with a 59-base RNA stem-loop structure, called the traus-activation region (Tar) at the 5 end of all nascent HlV-1 mRNA molecules, in order for the vims to replicate. HIV-Tat is actively transported across the cell membrane, and localizes to the nucleus [28]. It has been found that the arginine-rich Tar-binding region of the Tat protein, residues 49-57 (Tat+9 57), is primarily responsible for this translocation activity [29]. 

Figure 39-19. Structure of a typical eukaryotic mRNA showing elements that are involved in regulating mRNA stability. The typical eukaryotic mRNA has a 5 noncoding sequence (5 NCS), a coding region, and a 3 NCS. All are capped at the 5 end, and most have a polyadenylate sequence at the 3 end. The 5 cap and 3 poly(A) tail protect the mRNA against exonuclease attack. Stem-loop structures in the 5 and 3 NCS, features in the coding sequence, and the AU-rich region in the 3 NCS are thought to play roles in mRNA stability.

The efficiency of translation driven by IRES elements is often significandy lower than that of canonical translation (e.g., Fig. 6.1C) and, thus, control experiments may be needed to demonstrate that genuine IRES activity is measured. This can be done by inserting a stable stem-loop structure into the mRNA 5 UTR, upstream of the IRES element, or by comparing the translational output of a reporter mRNAs with the wild-type IRES to that of the equivalent transcript harboring a mutated, inactive IRES element (which should be much lower Humphreys et al, 2005 Wilson et al, 2000). 

While RNA molecules do not have the double stranded structure usually found in DNA, in many RNA molecules stem-loop structures are found in which the anti-parallel strands are connected by a 5-7 residue loop. Rather like the P-tum in proteins, this allows the... 

Palmer DK, O Day K, Margolis RL (1990) The centromere specific histone CENP-A is selectively retained in discrete foci in mattunaUan sperm nuclei. Chromosoma 100 32—36 Pandey NB, Marzluff WF (1987) The stem-loop structure at the 3 end of histone mRNA is necessary and sufficient for regulation of histone mRNA stabiUty. Mol Cell Biol 7 4557 559 Pehrson J, Fuji RN (1998) Evolutionary conservation of histone macroH2A subtypes and domains. Nucl Acids Res 26 2837-2842... 

The stem-loop structure in the noncoding 3 region of selenoprotein mRNAs has also been termed a SECTS element in mammals although it has a different overall structure. ° In silica analysis of the human genome sequence, using this consensus SECTS element along with the presence of the characteristic UGA codon within an exon, has led to the discovery of several new selenoproteins, including a selenium-dependent methionine sulfoxide reductase. It has been shown that a specific complex exists for selenoprotein synthesis that shuttles between the nucleus and the cytosol. This possibly protects the preformed complex for nonsense-mediated decay to allow for more efficient selenoprotein synthesis. The specific tRNA needed for selenocysteine... 

Figure 1. Consensus nucleotide sequence and stem-loop structure of hammerhead ribozyme.

Figure 5-9 The contribution of base-paired regions and loops to the Gibbs energy of a possible secondary structure for a 55 base fragment from R17 virus. The stem-loop structure shown here is part of a larger one considered by Tinoco et al.58...

The broad peaks B, D, and E are shifted far upfield by reaction with bisulfite (Eq. 5-11) suggesting that they are not hydrogen bonded and are present in the loop of the stem-loop structure. Peaks A, E, F, and G correspond to resonances 64, 7, 67, and 4, respectively, in (A) and represent fluorouracil in the stem structure. From Chu et al.69i Courtesy of Jack Horowitz. (C) A 31P NMR spectrum of a synthetic 14 base-pair DNA segment related to the E. coli lac operator. The palindromic sequence is TCTGAGCGCTCAGA. The numbers refer to the positions from the 5 end. From Schroeder et al.688... 

Aconitase exists as both mitochondrial and cytosolic isoenzyme forms of similar structure. However, the cytosolic isoenzyme has a second function. In its apoenzyme form, which lacks the iron-sulfur cluster, it acts as the much-studied iron regulatory factor, or iron-responsive element binding protein (IRE-BP). This protein binds to a specific stem-loop structure in the messenger RNA for proteins involved in iron transport and storage (Chapter 28).86/9°... 

TAR, a 59-residue stem-loop structure binding site for Tat... 

CCSL A Coiled-Coil Stem Loop Structure of de novo Design (1994)... 

Klug et al. (1999) selected RNA sequences that bind the Sel B protein of E. coli, an elongation factor which recognizes a stem-loop structure and drives the incorpor-ation of selenocysteine in response to an opal (UGA) codon immediately upstream of the structure. The wild-type hairpin recognized by Sel B in the dehydrogenase G mRNA was used as a competitor for the selection allowing the RNA pool to evolve very quickly. In four cycles high affinity aptamers (Kd 1 nM) were selected. Several aptamers bound 50-fold... 

E. coli has seven rRNA transcription units, each containing one copy each of the 23S, 16S and 5S rRNA genes as well as one to four tRNA genes. Transcription produces a 30S pre-rRNA transcript. This folds up to form stem-loop structures, ribosomal proteins bind, and a number of nucleotides become methylated. The modified pre-rRNA transcript is then cleaved at specific sites by RNase III and the ends are trimmed by ribonucleases M5, M6 and M23 to release the mature rRNAs. 

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