Oligonucleotides secondary structures

Pyne A, Thompson R, Leung C, Roy D, Hoogenboom BW. Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy. Small 2014 10 3257. 

Fig.l. The Hammerhead ribozyme. A Sequence and secondary structure. B Three dimensional structure of the HHR according to Scott et al. [33]. The substrate oligonucleotide (blue) is hybridized to the catalytic part (cyan)... 

Fig. 9. The transacetylase ribozyme. A Secondary structure of the clone 11 transacylase ribozyme based on the Zuker RNA folding algorithm Mfold. The oligonucleotide substrate is shaded in gray. The 2 -OH group of cytosine 147 (arrow) is the site of modification of the oligonucleotide substrate. B Reaction catalyzed by the clone 11 transacylase ribozyme. Note that the equilibrium of the reaction lies strongly on the side of the Bio-Phe-AMP substrate...

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-...

Mishra, R.K., Le Tinevez, R. and Toulme, J.J. (1996) Targeting nucleic acid secondary structures by antisense oligonucleotides designed through in vitro selection. Proc. Natl. Acad. Sci. USA, 93, 10679-10684. 

Poly(L-lysine) (PLL) Linear, tends to form secondary structures, primary amino groups Plasmid and oligonucleotide delivery, in vitro and in vivo (WuandWu, 1987, Wagner eto/., 1991)... 

In terms of physiological conditions, DNA exists almost totally in the double-helical conformation. Certain oligonucleotides also exhibit the ability to form triple-helixes with the DNA double strands. The stability of DNA secondary structures strongly depends on the environmental conditions, such as ionic strength, pH, temperature and solvents. Temperature is the most widely used environmental variable for the quantitative characterization of the helix-coil transitions. A commonly accepted characteristic of the thermal stability of DNA secondary structures is melting temperature, Tm. The binding of cationic species, such as multivalent... 

Figure 4.18. Graphic display of macromolecular interaction with Cn3D. The display window of Cn3D illustrates the 3D structure of Zn finger peptide fragments (secondary structure features) bound to the duplex oligonucleotides (brown backbone). Zinc atoms are depicted as spheres. The alignment window shows the amino acid sequence depicting the secondary structures (blue helices and arrows for a-helical and /J-strand structures, respectively) and interacting (thin brown arrows) residues. The structure file, 1A1K.val, is derived from lAAY.pdb.

Figure 8 shows the reconstructed histogram from an AX purification of DMT-off crude ISIS 2302, a 20 mer phosphorothioate oligonucleotide. A strong AX resin, in this case POROS HQ/50 (PE BioSystems), was used. Sample loading in related experiments varied from 5 to 10 g. High pH eluents prepared with NaOH were used to minimize secondary structure... 

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