Two-dimensional combinatorial screening identifies specific 6'-acylated kanamycin A- and 6'-acylated neamine-RNA hairpin interactions.
Herein, we report the RNA hairpin loops from a six-nucleotide hairpin library that bind 6'-acylated kanamycin A (1) and 6'-acylated neamine (2) identified by two-dimensional combinatorial screening (2DCS). Hairpins selected to bind 1 have K(d)'s ranging from 235 to 1035 nM, with an average K(d) of 618 nM. For 2, the selected hairpins bind with K(d)'s ranging from 135 to 2300 nM, with an average K(d) of 1010 nM. The selected RNA hairpin-ligand interactions are also specific for the ligand that they were selected to bind compared with the other arrayed ligand. For example, the mixture of hairpins selected for 1 on average bind 33-fold more tightly to 1 than to 2, while the mixtures of hairpins selected for 2 on average bind 11-fold more tightly to 2 than to 1. Secondary structure prediction of the selected sequences was completed to determine the motifs that each ligand binds, and the hairpin loop preferences for 1 and 2 were computed. For 1, the preferred hairpin loops contain an adenine separated by at least two nucleotides from a cytosine, for example, ANNCNN (two-tailed p-value = 0.0010) and ANNNCN (two-tailed p-value <0.0001). For 2, the preferred hairpin loops contain both 5'GC and 5'CG steps (two-tailed p-value <0.0001). These results expand the information available on the RNA hairpin loops that bind small molecules and could prove useful for targeting RNA.
Aminova
Olga
O
Department of Chemistry, University at Buffalo, The State University of New York, and the NYS Center of Excellence in Bioinformatics & Life Sciences, 657 Natural Sciences Complex, Buffalo, New York 14260, USA.
Paul
Dustin J
DJ
Childs-Disney
Jessica L
JL
Disney
Matthew D
MD
D000215:Acylation; D000225:Adenine; D001483:Base Sequence; D020650:Combinatorial Chemistry Techniques; D003596:Cytosine; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D005601:Framycetin / Q000737:chemistry* / Q000378:metabolism*; D055029:Inverted Repeat Sequences / Q000235:genetics*; D007612:Kanamycin / Q000737:chemistry* / Q000378:metabolism*; D008024:Ligands; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity
D008024:Ligands; D005601:Framycetin; D007612:Kanamycin; C488396:neamine; D012313:RNA; D003596:Cytosine; D000225:Adenine