Isolation of RNA Aptamers for Biological Cofactors by In Vitro Selection

A Novel, Modification-Dependent ATP-Binding Aptamer Selected from an RNA Library Incorporating a Cationic Functionality

“…Overall, the introduction of an amino functionality appears to have made surprisingly little difference to the outcome of these selection experiments. Both the modified RNA and DNA pools still allowed the emergence of the same receptor structures that were seen from the unmodified RNA and DNA pools (40,(56)(57)(58)62). We suspect that the full potential of these modifications to influence the results of a selection might not be seen until selective pressures are applied that cannot be overcome by normal RNA and DNA.…”

“…Selections for ATP-binding structures have now been carried out from a number of nucleic acids (RNA, DNA, aminopropyl-U RNA, and amino-propynyl-dU DNA, fluoresceinated U, and boronated derivatives) (40,(56)(57)(58)(62)(63)(64) and from a random sequence polypeptide library (65). It is of interest to compare the molecules that have emerged from these distinct libraries.…”

Discovering Human RNA Aptamers by Structure-Based Bioinformatics and Genome-Based In Vitro Selection

“…In principle, the pool can sample the entire genome of the target organism at single-nucleotide resolution (in both directions, with respect to the engineered RNA polymerase promoter), independent of expression of individual genes, but lacks sequences corresponding to spliced and otherwise processed transcripts. Structural characterization of the (Burgstaller & Famulok, 1994;Sassanfar & Szostak, 1993;Vu et al, 2012). The bulged guanosine nucleotide necessary for ligand binding is in bold.…”

“…2.2) used to find adenosine aptamers in the human genome are based on in vitro selected RNAs that bind adenosine containing molecules (Burgstaller & Famulok, 1994;Burke & Gold, 1997;Sassanfar & Szostak, 1993).…”

Recombination, RNA evolution, and bifunctional RNA molecules isolated through Chimeric SELEX

“…The "Chimeric SELEX" method described here simulates random recombination among functional RNAs derived from RNA populations with 70 or 80 positions of random sequence+ Specifically, we make use of previously described RNA populations that bind chloramphenicol [Cam ], adenosine , or coenzyme A [CoA (Burke & Hoffman, 1998)]+ These aptamers were selected from random initial pools that contained either 70 ("70N") or 80 ("80N") positions of random sequence+ Among the diverse sequences from the Cam-binding populations ("70Cm" and "80Cm"), there were some that contained the motif in Figure 1A, which has a weak but suggestive similarity to the portions of 23S rRNA involved in Cam binding and peptide bond formation )+ All of the isolates from the adenosine-binding population (80S), which was selected to recognize S-adenosyl methionine (SAM), conformed to the sequence motif shown in Figure 1B+ This element has also been isolated in selections for RNAs that bind ATP (Sassanfar & Szostak, 1993) and NAD ϩ (Burgstaller & Famulok, 1994), and it recognizes many other adenosine derivatives+ Of the two CoA-binding populations, the "80CoA" sequences were highly diverse, whereas the "70CoA" population was dominated by a motif that recruited secondary structural elements and 12 specifically required unpaired nucleotides from the primer binding sites (Fig+ 1C)+ This RNA element also binds many adenosine derivatives, but its specificity differs significantly from that of apta-FIGURE 1. Schematic representation of some of the aptamer modules used in this study+ A: One of the Cam-binding aptamer motifs present in both population 70Cm and 80Cm + B: Conserved adenosine-binding aptamer motif present in population 80S (Sassanfar & Szostak, 1993;Burgstaller & Famulok, 1994;+ C: Conserved CoA-binding aptamer motif found in population 70CoA (Burke & Hoffman, 1998)+ N, any nucleotide; n, its base pairing complement; x, variable number of nucleotides of any sequence+ Nucleotides that were intolerant of mutations or were highly conserved are in bold print+ mers from the 80S population+ The 70CoA and 80CoA populations also contained low frequencies of RNAs that required intact CoA for elution from the CoA resin and were not eluted by AMP alone (Burke & Hoffman, 1998)…”