Coaxial stacking Nucleic acid tertiary structure

secondary (inset) , tertiary structure of trna demonstrating coaxial stacking.

coaxial stacking, otherwise known helical stacking, major determinant of higher order rna tertiary structure. coaxial stacking occurs when 2 rna duplexes form contiguous helix, stabilized base stacking @ interface of 2 helices. coaxial stacking noted in crystal structure of trnaphe. more recently, coaxial stacking has been observed in higher order structures of many ribozymes, including many forms of self-splicing group , group ii introns. common coaxial stacking motifs include kissing loop interaction , pseudoknot. stability of these interactions can predicted adaptation of “turner’s rules”.

in 1994, walter , turner determined free energy contributions of nearest neighbor stacking interactions within helix-helix interface using model system created helix-helix interface between short oligomer , four-nucleotide overhang @ end of hairpin stem . experiments confirmed thermodynamic contribution of base-stacking between 2 helical secondary structures closely mimics thermodynamics of standard duplex formation (nearest neighbor interactions predict thermodynamic stability of resulting helix). relative stability of nearest neighbor interactions can used predict favorable coaxial stacking based on known secondary structure. walter , turner found that, on average, prediction of rna structure improved 67% 74% accuracy when coaxial stacking contributions included. turner , colleagues later used explicit quantification of stacking based on x-ray crystal structure databases define such stacking , study kinetics in molecular dynamics simulations. theories of coaxial stacking can tested using technique of helical fusion. approach used murphy , cech confirm coaxial stacking interaction between p4 , p6 helices within catalytic center of tetrahymena group intron.

most well-studied rna tertiary structures contain examples of coaxial stacking. prominent examples trna-phe, group introns, group ii introns, , ribosomal rnas. crystal structures of trna revealed presence of 2 extended helices result coaxial stacking of amino-acid acceptor stem t-arm, , stacking of d- , anticodon-arms. these interactions within trna orient anticodon stem perpendicularly amino-acid stem, leading functional l-shaped tertiary structure. in group introns, p4 , p6 helices shown coaxially stack using combination of biochemical , crystallographic methods. p456 crystal structure provided detailed view of how coaxial stacking stabilizes packing of rna helices tertiary structures. in self-splicing group ii intron oceanobacillus iheyensis, ia , ib stems coaxially stack , contribute relative orientation of constituent helices of five-way junction. orientation facilitates proper folding of active site of functional ribozyme. ribosome contains numerous examples of coaxial stacking, including stacked segments long 70 bp.

formation of pseudoknot coaxial stacking of 2 helices

two common motifs involving coaxial stacking kissing loops , pseudoknots. in kissing loop interactions, single-stranded loop regions of 2 hairpins interact through base pairing, forming composite, coaxially stacked helix. notably, structure allows of nucleotides in each loop participate in base-pairing , stacking interactions. motif visualized , studied using nmr analysis lee , crothers. pseudoknot motif occurs when single stranded region of hairpin loop basepairs upstream or downstream sequence within same rna strand. 2 resulting duplex regions stack upon 1 another, forming stable coaxially stacked composite helix. 1 example of pseudoknot motif highly stable hepatitis delta virus ribozyme, in backbone shows overall double pseudoknot topology.

an effect similar coaxial stacking has been observed in rationally designed dna structures. dna origami structures contain large number of double helixes exposed blunt ends. these structures observed stick along edges contained these exposed blunt ends, due hydrophobic stacking interactions.