Helical junctions

The hammerhead motif has a conserved secondary structure consisting of a three-way helical junction. The helical elements may vary in base sequence among species but thirteen bases at the three-way helical junction are conserved and essential for ribozyme activity. X-ray structures to be discussed below define a domain organization based on the tertiary folding observed in... 

These results lead to a conclusion that the visible C NMR peaks are due to the single helical portion. The NMR-invisible portion of the gel is present as multi-helical junction-zones. 

The Analysis of Helical Junctions Using the Long-Short... 

Helical branchpoints, or junctions, abound in natural RNA molecules, where they connect helical segments (Lilley, 2000). Three- and fourway helical junctions are common elements in small, autonomously folding RNA species such as several of the nucleolytic ribozymes, and have also been selected by a number of riboswitches to create pockets that selectively... 

There have been a number of refinements to the theory (Barkema el al., 1994 Duke et al., 1992 Lerman and Frisch, 1982 Levene and Zimm, 1989 Lumpkin et al., 1985, 1989), to include nucleic acid elasticity for example (Deutsch, 1988). There is no well-developed theory at the present time for nucleic acids containing helical junctions, although there have been recent attempts to incorporate this (Heuer et al., 2005 Saha et al., 2006). However, most electrophoretic data on junctions are analyzed empirically. The general rule that increased kinking results in lower mobility seems to work well, unless bending is so severe that helices clash (see, e.g., Goody et al., 2003). The very basis of the comparative approach is that the conclusions result from the interpretation of relative mobilities of matched species. 

Helical junctions are structures in which a number of helical segments are connected by the covalent continuity of strands shared between them. There may or may not be additional unpaired nucleotides present at the positions where the strands exchange between the helices. These are named according to the IUB nomenclature (Lilley et al., 1995). 

Lilley, D. M.J. (2000). Structures of helical junctions in nucleic acids. Quart. Rev. Biophys. 33, 109-159. 

Another prediction of reptation theory is that molecules move fastest when the entire chain is in the same tube. Partial unfolding or branching of the helix makes this less likely, and consequently impede migration, resulting in anomalous migration patterns that can be used to model helical junctions and bend angles (Lilley, 2008 Zinkel and Crothers, 1990). 

The three-way helical junctions all play key roles in directing the architecture of the ribozyme. The low-resolution electron density envelope is good enough to fit cylindrical representations of helical segments and has provided a starting point for more detailed structural modeling of the VS ribozyme to include the junctions and tertiary interactions. 

Theimer, C. A., and Giedroc, D. P. (2000). Contribution of the intercalated adenosine at the helical junction to the stability of the gag-pro frameshifting pseudoknot from mouse mammary tumor virus. RNA 6, 409-421. 

The structure of the pbuE leader RNA is similar to the guanine-dependent RNA sensor in the xpt leader transcript (65). It was shown that a single C to U substitution in the loop of a triple helical junction swapped the xpt aptamer specificity from guanine to adenine. Importantly, the pbuE leader contains a U in the identical position. These results led to the hypothesis that this U residue in the pbuE leader base-paired with adenine, whereas the C residue in the xpt transcript paired with guanine This hypothesis was verified by NMR structural studies. Moreover, it was determined that adenine binding to pbuE leader RNA involved a base triple with two U residues, which includes the previously proposed uridine (68). 

The core of the hairpin ribozyme comprises two formally unpaired loops carried on adjacent arms of a four-way helical junction. The junction is not essential to the activity, but provides efficient folding to create a local structure that approximates in-line geometry for the attacking 2 -OH of the adenosine residue. In common with the structure of the hammerhead, the scissile bond, which is cleaved to a 2, 3 -cyclic phosphate, is unpaired and is bounded by helical regions. 

Agarose is a linear pol5mer with a molecular mass of about 120 000. The agarose gel contains double helices, stabilized by the presence of water molecules hound inside the double-helical cavity. It seems that this network model is excessive and that only a small proportion of douhle-helical junction zones would be sufficient to realize the gelation process. This is why some authors consider that network structure of agarose gel consists of single chain [33, 34]. 

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