Recognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions

Cowan, J. A.

doi:10.1093/nar/28.15.2935

Cited by 72 publications

(71 citation statements)

References 27 publications

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“…RNA aptamers that specifically bound to neomycin-B over paromomycin were identified by in vitro selection (Wallis et al 1995) and this aptamer-ligand interaction has been studied intensively (Wallis and Schroeder 1997;Cowan et al 2000;de-los-Santos-Alvarez et al 2007Stampfl et al 2007). With the intent to use NEO1A in synthetic biology applications that would require that the aptamer be functional in the cell cytoplasm, we examined the interaction of NEO1A with its ligands in Buffer A that emulates the free ion concentrations of the mammalian cell cytoplasm.…”

Section: Discussionmentioning

confidence: 99%

“…The complex is stabilized by electrostatic and Hbonding interactions (Wallis and Schroeder 1997;Cowan et al 2000;de-los-Santos-Alvarez et al 2007Stampfl et al 2007). Our NMR results (performed in a similar buffer as the original study) are consistent with the reported structure of the neomycin-B-NEO1A complex.…”

Section: Discussionmentioning

confidence: 99%

“…The focus of the current study is a 23-nt RNA aptamer selected against neomycin-B (NEO1A), which is the smallest RNA motif reported to have high affinity and specificity for neomycin-B over paromomycin (Wallis et al 1995;Wallis and Schroeder 1997;Cowan et al 2000;de-los-SantosAlvarez et al 2007de-los-SantosAlvarez et al , 2009Stampfl et al 2007). An NMR-derived structure is available for the NEO1A in complex with neomycin-B (Jiang et al 1999) but there is no equivalent structure for the apo-aptamer.…”

Section: Introductionmentioning

confidence: 99%

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

İlgü

Fulton²,

Yennamalli

et al. 2014

RNA

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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 wellstructured 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.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

İlgü

Fulton²,

Yennamalli

et al. 2014

RNA

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“…Wang & Rando, 1995) Tobramycin 2'-OMe-RNA Electrochemical (Impedence) 0.7 µM (González-Fernández et al, 2011) RNA 180 -- (Kwon et al, 2001) Kanamycin RNA 10-30 -- (Goertz, Colin Cox Ellington, 2004b) RNA Low nM -- (Goertz, Colin Cox Ellington, 2004b) RNA 1800 -- (Cowan et al, 2000) Electrochemical (Impedence) "sub µM" (de-los-Santos-Alvarez et al, 2007) Neomycin 2'-OMe-RNA Surface Plasmon Resonance (SPR) 10 nM (de-los-Santos-Álvarez et al, 2009) - (Cruz-Aguado & Penner, 2008a) Fluorescence Polarization 5 nM (Cruz-Aguado & Penner, 2008b) Electrochemical 30 pg/mL (Kuang et al, 2010) Electrochemiluminescent 0.007 ng/mL (Z. Wang et al, 2010) Mycotoxins Ochratoxin A DNA 200…”

Section: Aminoglycosidesmentioning

confidence: 99%

Advances in Aptamer-Based Biosensors for Food Safety

McKeague¹,

Giamberardino²,

DeRosa³

2011

Environmental Biosensors

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“…Aptamers are particularly attractive as therapeutics since they are not immunogenic, can be chemically synthesized and are amenable to chemical modifications (Kusser 2000). Target-specific aptamers are created through SELEX Piasecki et al 2009) against many types of targets, ranging from small organic molecules like neomycin (Cowan et al 2000), viral peptides like HIV-1 Rev (Ye et al 1999), to large macromolecules such as thrombin (Macaya et al 1993). Of the hundred odd aptamer structures that have been deposited into the PDB, only six are protein-RNA aptamer complexes, 2 and only three of these represent proteins that do not natively bind nucleic acids.…”

Section: Introductionmentioning

confidence: 99%

An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates

Padlan

Malashkevich

Almo

et al. 2014

RNA

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RNA aptamers are being developed as inhibitors of macromolecular and cellular function, diagnostic tools, and potential therapeutics. Our understanding of the physical nature of this emerging class of nucleic acid-protein complexes is limited; few atomic resolution structures have been reported for aptamers bound to their protein target. Guided by chemical mapping, we systematically minimized an RNA aptamer (Lys1) selected against hen egg white lysozyme. The resultant 59-nucleotide compact aptamer (Lys1.2minE) retains nanomolar binding affinity and the ability to inhibit lysozyme's catalytic activity. Our 2.0-Å crystal structure of the aptamer-protein complex reveals a helical stem stabilizing two loops to form a protein binding platform that binds lysozyme distal to the catalytic cleft. This structure along with complementary solution analyses illuminate a novel protein-nucleic acid interface; (1) only 410 Å 2 of solvent accessible surface are buried by aptamer binding; (2) an unusually small fraction (∼18%) of the RNA-protein interaction is electrostatic, consistent with the limited protein phosphate backbone contacts observed in the structure; (3) a single Na + stabilizes the loops that constitute the protein-binding platform, and consistent with this observation, Lys1.2minE-lysozyme complex formation takes up rather than displaces cations at low ionic strength; (4) Lys1.2minE inhibits catalysis of large cell wall substrates but not catalysis of small model substrates; and (5) the helical stem of Lys1.2minE can be shortened to four base pairs (Lys1.2minF) without compromising binding affinity, yielding a 45-nucleotide aptamer whose structure may be an adaptable protein binding platform.

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Recognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions

Cited by 72 publications

References 27 publications

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

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

Advances in Aptamer-Based Biosensors for Food Safety

An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates

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