Replicative form secondary structure

The Structure of DNA Elucidation of the three-dimensional structure of DNA helped researchers understand how this molecule conveys information that can be faithfully replicated from one generation to the next. Tb see the secondary structure of double-stranded DNA, go to the Protein Data Bank website (www.rcsb.org pdb). Use the PDB identifiers listed below to retrieve the data pages for the two forms of DNA... 

Figure 1. Catalysis and template action of RNA and proteins. Catalytic action of one RNA molecule on another one is shown in the simplest case, the "hammerhead ribozyme." The substrate is a tridecanucleotide forming two double-helical stacks together with the ribozyme (n = 34) in the confolded complex. Tertiary interactions determine the detailed structure of the hammerhead ribozyme complex and are important for the enzymatic reaction cleaving one of the two linkages between the two stacks. Substrate specificity of ribozyme catalysis is caused by secondary structure in the cofolded complex between substrate and catalyst. Autocatalytic replication of oligonucleotide and nucleic acid is based on G = C and A = U complementarity in the hydrogen bonded complexes of nucleotides forming a Watson-Crick type double helix. Gunter von Kiedrowski s experi-...

The enzyme processes template and newly synthesized strand in such a way that the formation of (plus-minus) double strands is avoided. The experimentally determined rate of RNA chain elongation is highly variable (Mills et al., 1978). The replicase stop temporarily at certain pause sites in order to allow formation or reformation of secondary structures. In particular, hairpin loops are formed in the product strand and reformed in the template strand. Thereby, the formation of RNA double strands is avoided. This is very important for efficient RNA synthesis. Double strands have to melt at least in part before they are recognized as templates by the enzyme. Biebricher et al. (1982) found a polynucleotide which exists in two defined secondary structures. The more stable configuration, presumably a hairpin with a long double stranded region, is very unefficient in replication. 

Therefore to make meaningful inferences from experiments such as those reported by Yamashita et al. either the error structure must be known or sufficient data must be provided, preferably in the form of optimally designed replicates. This analysis confirms that it is generally insufficient to evaluate only point estimates. In fact these are secondary to evaluating and reporting joint probability regions. 

Nevertheless, the RNA World hypothesis would seem to answer most of the questions raised above how can an essentially linear molecule be autocatalytic, how can it synthesize proteins, and how can it replicate Autocatalysis can occur because RNA can adopt a wide range of secondary and tertiary structures that position RNA monomers into a preorganized sequence and link them together, it can apply the same flexibility to bind other small molecules and catalyse their polymerization, and it could form weakly interacting sense and antisense duplexes. The main problem is... 

The A and B forms are relatively stable for RNA and DNA, respectively, under physiological conditions. They must not be too stable, however, because processes, such as DNA replication (see here) and transcription, cannot occur unless the double-helix structure can be opened up. Denaturation refers to the loss of secondary (or tertiary) structure over large regions of a polynucleotide. Forces favoring denaturation of polynucleotides include... 

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