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

Ilgu, M.; Fulton, D. B.; Yennamalli, R. M.; Lamm, M. H.; Sen, T. Z.; Nilsen-Hamilton, M.

doi:10.1261/rna.041145.113

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

Journal Article · Tue Apr 22 00:00:00 EDT 2014 · RNA

DOI:https://doi.org/10.1261/rna.041145.113· OSTI ID:1627094

Ilgu, M. ^[1]; Fulton, D. B. ^[2]; Yennamalli, R. M. ^[3]; Lamm, M. H. ^[4]; Sen, T. Z. ^[3]; Nilsen-Hamilton, M. ^[5]

Ames Lab., Ames, IA (United States); Iowa State Univ., Ames, IA (United States). Roy J. Carver Dept. of Biochemistry, Biphysics and Molecular Biology; DOE/OSTI
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
Iowa State Univ., Ames, IA (United States). Dept. of Chemical and Biologival Engineering
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

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.

View Accepted Manuscript (DOE)

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, Journal Name: RNA Journal Issue: 6 Vol. 20; ISSN 1355-8382

Publisher:: Cambridge University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (39)

Monovalent Ion Dependence of Neomycin B Binding to an RNA Aptamer Characterized by Spectroscopic Methods Stampfl, Sabine; Lempradl, Adelheid; Koehler, Gottfried ChemBioChem, Vol. 8, Issue 10 https://doi.org/10.1002/cbic.200700030	journal	July 2007
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Inhibition of the Self-cleavage Reaction of the Human Hepatitis Delta Virus Ribozyme by Antibiotics Rogers, Jeff; Chang, Alex H.; von Ahsen, Uwe Journal of Molecular Biology, Vol. 259, Issue 5 https://doi.org/10.1006/jmbi.1996.0369	journal	June 1996
Inhibition of hepatitis delta virus genomic ribozyme self-cleavage by aminoglycosides Chia, Ju-Shin; Wu, Hui-Lin; Wang, Hsei-Wei Journal of Biomedical Science, Vol. 4, Issue 5 https://doi.org/10.1007/BF02253420	journal	September 1997
A geometric approach to macromolecule-ligand interactions Kuntz, Irwin D.; Blaney, Jeffrey M.; Oatley, Stuart J. Journal of Molecular Biology, Vol. 161, Issue 2 https://doi.org/10.1016/0022-2836(82)90153-X	journal	October 1982
Non-competitive inhibition of group I intron RNA self-splicing by aminoglycoside antibiotics von Ahsen, Uwe; Davies, Julian; Schroeder, Renée Journal of Molecular Biology, Vol. 226, Issue 4 https://doi.org/10.1016/0022-2836(92)91043-O	journal	August 1992
The functional role of ribosomal RNA in protein synthesis Dahlberg, Albert E. Cell, Vol. 57, Issue 4 https://doi.org/10.1016/0092-8674(89)90122-0	journal	May 1989
Small molecules that selectively block RNA binding of HIV-1 rev protein inhibit rev function and viral production Zapp, Maria L.; Stern, Seth; Green, Michael R. Cell, Vol. 74, Issue 6 https://doi.org/10.1016/0092-8674(93)90720-B	journal	September 1993
Specific binding of aminoglycoside antibiotics to RNA Wang, Yong; Rando, Robert R. Chemistry & Biology, Vol. 2, Issue 5 https://doi.org/10.1016/1074-5521(95)90047-0	journal	May 1995
In vitro selection of RNA lectins: using combinatorial chemistry to interpret ribozyme evolution Lato, Susan M.; Boles, Amy R.; Ellington, Andrew D. Chemistry & Biology, Vol. 2, Issue 5 https://doi.org/10.1016/1074-5521(95)90048-9	journal	May 1995
A novel RNA motif for neomycin recognition Wallis, Mary G.; von Ahsen, Uwe; Schroeder, Renee Chemistry & Biology, Vol. 2, Issue 8 https://doi.org/10.1016/1074-5521(95)90188-4	journal	August 1995
The binding of antibiotics to RNA Wallis, Mary G.; Schroeder, Renée Progress in Biophysics and Molecular Biology, Vol. 67, Issue 2-3 https://doi.org/10.1016/S0079-6107(97)00011-4	journal	January 1997
Saccharide–RNA recognition in a complex formed between neomycin B and an RNA aptamer Jiang, Licong; Majumdar, Ananya; Hu, Weidong Structure, Vol. 7, Issue 7 https://doi.org/10.1016/S0969-2126(99)80105-1	journal	July 1999
Deciphering RNA recognition: aminoglycoside binding to the hammerhead ribozyme Tor, Yitzhak; Hermann, Thomas; Westhof, Eric Chemistry & Biology, Vol. 5, Issue 11 https://doi.org/10.1016/S1074-5521(98)90286-1	journal	November 1998
Dynamics of an anti-VEGF DNA aptamer: A single-molecule study Nick Taylor, J.; Darugar, Qusai; Kourentzi, Katerina Biochemical and Biophysical Research Communications, Vol. 373, Issue 2 https://doi.org/10.1016/j.bbrc.2008.05.191	journal	August 2008
SPR sensing of small molecules with modified RNA aptamers: Detection of neomycin B de-los-Santos-Álvarez, Noemí; Lobo-Castañón, María Jesús; Miranda-Ordieres, Arturo J. Biosensors and Bioelectronics, Vol. 24, Issue 8 https://doi.org/10.1016/j.bios.2009.01.011	journal	April 2009
RNA dynamics: it is about time Al-Hashimi, Hashim M.; Walter, Nils G. Current Opinion in Structural Biology, Vol. 18, Issue 3 https://doi.org/10.1016/j.sbi.2008.04.004	journal	June 2008
Investigating the malleability of RNA aptamers Ilgu, Muslum; Wang, Tianjiao; Lamm, Monica H. Methods, Vol. 63, Issue 2 https://doi.org/10.1016/j.ymeth.2013.03.016	journal	September 2013
Fluorescent nucleic acid base analogues Wilhelmsson, L. Marcus Quarterly Reviews of Biophysics, Vol. 43, Issue 2 https://doi.org/10.1017/S0033583510000090	journal	May 2010
Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies Nordlund, T. M.; Andersson, S.; Nilsson, L. Biochemistry, Vol. 28, Issue 23 https://doi.org/10.1021/bi00449a021	journal	November 1989
RNA Molecules That Specifically and Stoichiometrically Bind Aminoglycoside Antibiotics with High Affinities ^† Wang, Yong; Killian, Jennifer; Hamasaki, Keita Biochemistry, Vol. 35, Issue 38 https://doi.org/10.1021/bi960878w	journal	January 1996
Specificity of Aminoglycoside Binding to RNA Constructs Derived from the 16S rRNA Decoding Region and the HIV-RRE Activator Region Wang, Yong; Hamasaki, Keita; Rando, Robert R. Biochemistry, Vol. 36, Issue 4 https://doi.org/10.1021/bi962095g	journal	January 1997
Binding of Neomycin to the TAR Element of HIV-1 RNA Induces Dissociation of Tat Protein by an Allosteric Mechanism ^† Wang, Shaohui; Huber, Paul W.; Cui, Mei Biochemistry, Vol. 37, Issue 16 https://doi.org/10.1021/bi972808a	journal	April 1998
Aminoglycoside Antibiotics Are Able To Specifically Bind the 5‘-Untranslated Region of Thymidylate Synthase Messenger RNA ^† Tok, Jeffrey B. -H.; Cho, Junhyeong; Rando, Robert R. Biochemistry, Vol. 38, Issue 1 https://doi.org/10.1021/bi9819428	journal	January 1999
An Approach To Enhance Specificity against RNA Targets Using Heteroconjugates of Aminoglycosides and Chloramphenicol (or Linezolid) Lee, Jongkook; Kwon, Miyun; Lee, Kyung Hyun Journal of the American Chemical Society, Vol. 126, Issue 7 https://doi.org/10.1021/ja038937y	journal	January 2004
Modified-RNA Aptamer-Based Sensor for Competitive Impedimetric Assay of Neomycin B de-los-Santos-Álvarez, Noemí; Lobo-Castañón, María Jesús; Miranda-Ordieres, Arturo J. Journal of the American Chemical Society, Vol. 129, Issue 13 https://doi.org/10.1021/ja0689482	journal	March 2007
Interaction of antibiotics with functional sites in 16S ribosomal RNA Moazed, Danesh; Noller, Harry F. Nature, Vol. 327, Issue 6121 https://doi.org/10.1038/327389a0	journal	June 1987
Antibiotic inhibition of group I ribozyme function von Ahsen, Uwe; Davies, Julian; Schroeder, Renée Nature, Vol. 353, Issue 6342 https://doi.org/10.1038/353368a0	journal	September 1991
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure Mathews, D. H.; Disney, M. D.; Childs, J. L. Proceedings of the National Academy of Sciences, Vol. 101, Issue 19 https://doi.org/10.1073/pnas.0401799101	journal	May 2004
Base pairing and mutagenesis: observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR. Sowers, L. C.; Fazakerley, G. V.; Eritja, R. Proceedings of the National Academy of Sciences, Vol. 83, Issue 15 https://doi.org/10.1073/pnas.83.15.5434	journal	August 1986
Inhibition of RNase P RNA cleavage by aminoglycosides Mikkelsen, N. E.; Brannvall, M.; Virtanen, A. Proceedings of the National Academy of Sciences, Vol. 96, Issue 11 https://doi.org/10.1073/pnas.96.11.6155	journal	May 1999
Recognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions Cowan, J. A. Nucleic Acids Research, Vol. 28, Issue 15 https://doi.org/10.1093/nar/28.15.2935	journal	August 2000
Mechanistic insights into an engineered riboswitch: a switching element which confers riboswitch activity Weigand, Julia E.; Schmidtke, Sina R.; Will, Tristan J. Nucleic Acids Research, Vol. 39, Issue 8 https://doi.org/10.1093/nar/gkq946	journal	December 2010
Conformational dynamics of the tetracycline-binding aptamer Förster, Ute; Weigand, Julia E.; Trojanowski, Peter Nucleic Acids Research, Vol. 40, Issue 4 https://doi.org/10.1093/nar/gkr835	journal	November 2011
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Wallace, Andrew C.; Laskowski, Roman A.; Thornton, Janet M. "Protein Engineering, Design and Selection", Vol. 8, Issue 2 https://doi.org/10.1093/protein/8.2.127	journal	January 1995
Controlling Gene Expression in Living Cells Through Small Molecule-RNA Interactions Werstuck, G. Science, Vol. 282, Issue 5387 https://doi.org/10.1126/science.282.5387.296	journal	October 1998
Aspects of Bacterial Response to the Ionic Environment Brown, A. D. Bacteriological Reviews, Vol. 28, Issue 3 https://doi.org/10.1128/br.28.3.296-329.1964	journal	September 1964
Physiological and genetic responses of bacteria to osmotic stress Csonka, L. N. Microbiological Reviews, Vol. 53, Issue 1 https://doi.org/10.1128/mr.53.1.121-147.1989	journal	March 1989
DOCK 6: Combining techniques to model RNA-small molecule complexes Lang, P. T.; Brozell, S. R.; Mukherjee, S. RNA, Vol. 15, Issue 6 https://doi.org/10.1261/rna.1563609	journal	April 2009

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59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
aminoglycoside
aptamer
structure

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

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