Study of RNA structure by affinity cleaving

by Han, Hogyu

Abstract (Summary)
NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. Chapter 1. Sequence-specific recognition of double helical RNA and RNAâ¢DNA by triple helix formation. The stabilities of eight triple helical pyrimidineâ¢purineâ¢pyrimidine structures comprised of identical sequence but different RNA (R) or DNA (D) strand combinations were measured by quantitative affinity cleavage titration. The differences in equilibrium binding affinities reveal the importance of strand composition. For the sequences studied here, the stabilities of complexes containing a pyrimidine third strand D or R and purineâ¢pyrimidine double helical DD, DR, RD, and RR decrease in order: D + DD, R + DD, R + DR, D + DR > R + RD,R + RR >> D + RR,D + RD (pH 7.0, 25°C, 100 mM NaCl / 1mM spermine). These findings suggest that RNA and DNA oligonucleotides will be useful for targeting (i) double helical DNA and (ii) RNAâ¢DNA hybrids if the purine Watson-Crick strand is DNA. However, RNA, but not DNA, oligonucleotides will be useful for sequence-specific binding of (i) double helical RNA and (ii) RNAâ¢DNA hybrids if the purine Watson-Crick strand is RNA. This has implications for the design of artificial ligands targeted to specific sequences of double helical RNA and RNAâ¢DNA hybrids. Chapter 2. Different conformational families of pyrimidineâ¢purineâ¢pyrimidine triple helices depending on backbone composition. Different helical conformations of DNA (D), RNA (R), and DNAâ¢RNA (DR) hybrid double and triple helices have been detected using affinity cleavage analysis. Synthetic methods were developed to attach EDTAâ¢Fe to a single nucleotide on RNA as well as DNA oligonucleotides. Cleavage patterns generated by a localized diffusible oxidant in the major groove on the pyrimidine strand of four purineâ¢pyrimidine double helices consisting of all DNA, all RNA, and the corresponding hybrids reveal that the relative cleavage intensity shifts to the 5' end of the purine strand increasingly in the order: DDBibliographical Information:

Advisor:John Abelson; Carl Stevens Parker; Judith L. Campbell; Peter B. Dervan

School:California Institute of Technology

School Location:USA - California

Source Type:Master's Thesis



Date of Publication:03/03/1994

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