Recognition of duplex DNA by RNA polynucleotides

Selection of RNAs that Bind to Duplex DNA at Neutral pH

“…C-1). These data are in agreement with previous observations that a 140 nt unselected RNA containing a single copy of this 21 nt pyrimidine recognition sequence bound the DNA target sequence 650-fold less tightly than S (McDonald & Maher, 1995).…”

“…It is evident that these RNAs have been selected for binding to the DNA target sequence via conventional triple helix formation as has been observed (Pei et al, 1991). It is interesting to note that there appears to be no correlation between the number of cytosine residues present in the pyrimidine recognition sequences of selected RNAs pyrimidine recognition sequence designed to form a conventional triple helix with the DNA target (Maher et al, 1992;Skoog & Maher, 1993a,b;McDonald & Maher, 1995). The homopurine/ homopyrimidine target sequence ( Figure 1C) was designed such that it could be immobilized on a streptavidin/agarose support via a biotin linkage.…”

“…However, mildly acid conditions are often required for strong binding. In addition, the pyrimidine recognition sequence must be optimally presented within a longer RNA transcript (McDonald & Maher, 1995). Thus, expression of RNA transcripts containing potential repressor sequences does not guarantee their ability to function in vivo.…”

Selection and characterization of anti-NF-κB p65 RNA aptamers

“…Radiolabeled RNA was purified by denaturing polyacrylamide gel electrophoresis. Partial alkaline hydrolysis ladders were prepared at pH 8.3, and G-specific ladders were created using RNase T 1 (Epicentre) at 52°C in the presence of urea, as described (McDonald and Maher 1995). For probing the presence of single-stranded RNA, mung bean nuclease (1 U, New England Biolabs) was added to RNA (z100,000 cpm) in 50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl 2 , 1 mM DTT (pH 7.9) at 30°C for 1 min prior to addition of urea loading buffer and freezing on dry ice.…”

Evidence from CD spectra and melting temperatures for stable Hoogsteen-paired oligomer duplexes derived from DNA and hybrid triplexes

“…The two major nucleic acid triple-helix motifs with Hoogsteen or reverse Hoogsteen pairing of a third strand to a DNA duplex and the numerous ways in which a third strand might inhibit transcription or mediate mutagenesis and recombination in antigene drug therapies have been reviewed (1)(2)(3). There is evidence that triplexes can form under in vivo conditions (4)(5)(6)(7)(8)(9)(10)(11) and may involve RNA (12). With RNA as one or more of the strands, triple helix formation could potentially be used to control biological processes that encompass mRNA, RNA•DNA hybrids or RNA hairpins.…”