Nucleic Acid Fold

The nucleotide sequence of a nucleic acid immediately provides plausible models for the approximate secondary structures. The base-pairing patterns, A-T(U) and G-C, are easy to identify and several simple rules can guide selection of folding patterns  

In RNA, the original set consisting of the Watson-Crick base pairs is complemented by the G-U wobble pair, which is admissible in RNA double helices. Other admissible bps include U-U in internal loops as well as A-A, G-A or G-G (purine-purine closing pairs) at the ends of double helical regions or in multiloops. The secondary structures, which can be drawn in two dimensions without knots or pseudoknots, are indispensable for the 

The evolutionary approach performs comparative sequence analysis leading to models of the phylogenetic/physiologically active structures (Gutell, 1993). 

The task of assigning a plausible pattern of base pairing is greatly simplified if sequences are available for different species of RNA known to possess similar structures and functions. For example, the cloverleaf structure and the L-shaped fold have served as good approximations for modeling the secondary and tertiary structures of tRNA respectively. DNA and RNA sequences can be submitted to respective DNA mfold (http //bioinfo.math.rpi.edu/ nnfold/dna) and RNA mfold (http //bioinfo.math.rpi.edu/ mfold/ma) for fold predictions. 

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Zuker, M., Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res. 2003, 31, 3406 3415... 

Because conformational changes in RNA or short DNAs typically cause small changes in electrophoretic mobility, analysis of nucleic acid folding requires careful optimization of electrophoresis conditions. By contrast, protein—nucleic acid interactions are typically easier to analyze by native PAGE because the molecular weight and positive charge of the protein produces a relatively large shift in gel mobility. 

Tempcrature-jump methods have not been used in soil science. However, they have been widely employed in many areas of chemistry and biochemistry research to study the following types of reactions (Turner, 1986) electron transfer, enzyme catalysis, metal complex formation, nucleic acid folding, proton transfer, spin equilibria, and protein-ligand binding. 

The Study of Nucleic Acid Folding and Heteroduplex Formation. . 54... 

N.R. Markham, M. Zuker, UNAFold software for nucleic acid folding and hybridization, Methods Mol. Biol. (Clifton, NJ) 453 (2008) 3-31. 

Nickel Complexes as Probes of Guanine Sites in Nucleic Acid Folding... 

Markham, N.R. and Zuker, M. UNAFold—Software for nucleic acid folding and hybridization. Methods in Molecular Biology Volume II Structure, Function and Applications 453,3-31,2008. 

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