Coaxial Stacks and Multibranch Loops or Junctions

Coaxial stacking can occur when two helices are directly adjacent or separated by a mismatch. Coaxial stacks have been seen in crystal structures of tRNAs11-13'156'157 and are essential for the three-dimensional shape of tRNA. Stability increments from coaxial stacking of Watson-Crick pairs and of GA or CC mismatches have been investigated in model systems where a short oligomer binds to a four- or five-nucleotide overhang at the base of a hairpin stem.52'158'159 This binding creates an...

Secondary Structure Formation

Formation of double helix requires a nucleation event to bring the complementary regions of the sequence together, so the overall rate of forming a double helix is much slower than the rate of helix growth. If the reaction is bimolecular, the rate is governed by a corresponding rate constant that is typically in the range of 106 to 107 M_1 s-1.23,24 With a strand concentration of 1 iM, the characteristic time for helix formation is thus roughly 100 ms to 1 s. Hairpin helix formation is...

Conclusions

10.9.1 Natural Ribozymes and Selection Structure Determination The benefits of artificial phylogenetic analyses for nucleic acid structure prediction become apparent when RNA and protein catalysts are compared. The primary sequence of both types of biopolymers determines their global architecture, which in turn determines their catalytic functions. However, protein folds are determined partially by the formation of secondary structural elements, and largely by the establishment of tertiary...

Replication Of Viroids

12.6.1 Rolling Circle Mechanism of Replication There seems to be universal agreement that viroids are replicated by a rolling circle mechanism, as first proposed in 198440 (Figure 8), and the finer aspects of their replication are slowly being unraveled. In one of the two variations of the rolling circle mechanism (Figure 8(a)), the infectious plus RNA is copied continuously by an RNA polymerase to produce a long minus RNA strand. Specific cleavage of the ( ) strand, either enzymatically or RNA...

The Rate Of Base Pairing

Formation of a base pair is the elementary reaction step in the transfer of genetic information. Because of the cooperative character of double helix formation, the dynamic and equilibrium properties of base pairs differ greatly depending on whether they are located at the end of a helix or in its interior. Base pairs at the end of a helix open and close rapidly in a process called fraying, which has an equilibrium constant of roughly 2-10, depending on the nature of the base pair and its...

Editing By Base Modification

RNA modifications have long been known to occur in tRNAs, rRNAs, and mRNAs.4'5 Some of these modifications are simple, involving merely the methylation of an existing nucleotide, while others are quite complex, involving multiple enzymes for their synthesis. As additional types of RNA editing are discovered, it becomes harder to distinguish the difference between what has traditionally been called an RNA modification, from what is now categorized as RNA editing. At one point in time the term...

Structure And Evolution Of The Rna Subunit

The RNA subunit of RNase P from Bacteria has been characterized in many strains. The RNase P database,7 maintained by Dr. James Brown (North Carolina State University URL http www.mbio. ncsu.edu RnaseP home.html), contains almost 200 sequences of bacterial RNase P RNAs in addition to representatives of all other main phylogenetic groups. Once the first RNase P RNA genes were identified, additional ones were isolated by heterologous hybridization, analysis of genome databases and PCR...

Other Applications Of Nucleotide Modifications

Alternative strategies to those described above, that also make use of base modifications in RNA, have been successfully applied to investigate both structural and functional aspects of RNA. These include interference experiments, site-selected insertion of defined modified residues and exploiting the presence of enzyme-catalyzed modified nucleotides in natural RNAs. Interference experiments are aimed to identify at once those elements within an RNA that are involved in a functional process...

Info

Figure 2 The apoB mRNA editing reaction. The upper part of the figure shows the editing site cytidine red in the context of the sequences immediately surrounding the editing site that are important for the reaction. The three different regions that have been determined to be important for editing are boxed regulator, spacer, and mooring sequence, see text for details . The lower section of the figure illustrates the consequences of editing apoB mRNA. A glutamine codon is changed to a stop codon...