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Title: An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures

Journal Article · · RNA
 [1];  [2];  [3];  [4];  [3];  [5]
  1. Ames Lab., Ames, IA (United States); Iowa State Univ., Ames, IA (United States). Roy J. Carver Dept. of Biochemistry, Biphysics and Molecular Biology
  2. Iowa State Univ., Ames, IA (United States). Roy J. Carver Dept. of Biochemistry, Biphysics and Molecular Biology
  3. Iowa State Univ., Ames, IA (United States). Dept. of Genetics, Development and Cell Biology
  4. Iowa State Univ., Ames, IA (United States). Dept. of Chemical and Biologival Engineering
  5. Ames Lab., Ames, IA (United States); Iowa State Univ., Ames, IA (United States). Roy J. Carver Dept. of Biochemistry, Biphysics and Molecular Biology; Iowa State Univ., Ames, IA (United States). Dept. of Genetics, Development and Cell Biology
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Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP) fluorescence studies of the aptamer identified a flexible pentaloop and a stable binding pocket. Consistent with a well structured binding pocket, docking analysis results correlated with experimental measures of the binding energy for most ligands. Steady state fluorescence studies of 2AP-substituted aptamers confirmed that A16 moves to a more solvent accessible position upon ligand binding while A14 moves to a less solvent accessible position, which is most likely a base stack. Analysis of binding affinities of NEO1A sequence variants showed that the base in position 16 interacts differently with each ligand and the interaction is a function of the buffer constituents. Our results show that the pentaloop provides NEO1A with the ability to adapt to external influences on its structure, with the critical base at position 16 adjusting to incorporate each ligand into a stable pocket by hydrophobic interactions and/or hydrogen bonds depending on the ligand and the ionic environment.

Research Organization:
Iowa State Univ., Ames, IA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-07CH11358
OSTI ID:
1627094
Journal Information:
RNA, Vol. 20, Issue 6; ISSN 1355-8382
Publisher:
Cambridge University PressCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (4)

Common Secondary and Tertiary Structural Features of Aptamer–Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences journal December 2019
Fluorescent Aptamers for Detection and Treatment of Pathogenic Bacteria and Cancer posted_content January 2021
A self-assembling RNA aptamer-based nanoparticle sensor for fluorometric detection of Neomycin B in milk journal March 2016
Aptamers in analytics journal January 2016

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
aminoglycoside
aptamer
structure