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

Date

2014-06-01

Author

İlgü, Müslüm
Yennamalli, Ragothaman M.
Lamm, Monica H.
Sen, Taner Z.
Nilsen-Hamilton, Marit

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

54
views

0
downloads

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.

Subject Keywords

Molecular Biology

URI

https://hdl.handle.net/11511/46314

Journal

RNA

DOI

https://doi.org/10.1261/rna.041145.113

Collections

Department of Biology, Article

Suggestions

OpenMETU
Core

Investigating the malleability of RNA aptamers İlgü, Müslüm; Lamm, Monica H.; Nilsen-Hamilton, Marit (Elsevier BV, 2013-09-15) Aptamers are short, single-stranded nucleic acids with structures that frequently change upon ligand binding and are sensitive to the ionic environment. To achieve facile application of aptamers in controlling cellular activities, a better understanding is needed of aptamer ligand binding parameters, structures, intramolecular mobilities and how these structures adapt to different ionic environments with consequent effects on their ligand binding characteristics. Here we discuss the integration of biochemic...
The Karyote® Physico-Chemical Genomic, Proteomic, Metabolic Cell Modeling System Ortoleva, P.; Berry, E.; Brun, Y.; Fan, J.; Fontus, M.; Hubbard, K.; Jaqaman, K.; Jarymowycz, L.; Navid, A.; Sayyed-Ahmad, A.; Shreif, Z.; Stanley, F.; Tuncay, Kağan; Weitzke, E.; Wu, L.-C. (Mary Ann Liebert Inc, 2003-01-01) Modeling approaches to the dynamics of a living cell are presented that are strongly based on its underlying physical and chemical processes and its hierarchical spatio-temporal organization. Through the inclusion of a broad spectrum of processes and a rigorous analysis of the multiple scale nature of cellular dynamics, we are attempting to advance cell modeling and its applications. The presentation focuses on our cell modeling system, which integrates data archiving and quantitative physico-chemical model...
Using artificially generated spectral data to improve protein secondary structure prediction from Fourier transform infrared spectra of proteins Severcan, M; Haris, PI; Severcan, Feride (Elsevier BV, 2004-09-15) Secondary structures of proteins have been predicted using neural networks from their Fourier transform infrared spectra. To improve the generalization ability of the neural networks, the training data set has been artificially increased by linear interpolation. The leave-one-out approach has been used to demonstrate the applicability of the method. Bayesian regularization has been used to train the neural networks and the predictions have been further improved by the maximum-likelihood estimation method. T...
Prediction of hexagonal lattice parameters of various apatites by artificial neural networks Kockan, Umit; Evis, Zafer (International Union of Crystallography (IUCr), 2010-08-01) In this study, the hexagonal lattice parameters of apatite compounds, M-10(TO4)(6)X-2, where M is Na+, Ca2+, Ba2+, Cd2+, Pb2+, Sr2+, Mn2+, Zn2+, Eu2+, Nd3+, La3+ or Y3+, T is As+5, Cr+5, P5+, V5+ or Si+4, and X is F-, Cl-, OH- or Br-, were predicted from their ionic radii by artificial neural networks. A multilayer perceptron network was used for training and the best results were obtained with a Bayesian regularization method. Four neurons were used in the hidden layer, utilizing a tangent sigmoid activati...
IR and turbidity studies of vitamin E-cholesterol-phospholipid membrane interactions Severcan, Feride; Kazanci, Nadide; Baykal, Ülkü; Süzer, Şefik (Portland Press Ltd., 1995-8-1) Binary and tertiary mixture of α-tocophenol, cholesterol and dimyristoylphosphatidylcholine in the form of multilamellar liposomes were investigated by Fourier Transform Infrared and visible spectroscopy. Results of the FTIR and turbidity experiments indicate that α T decreases or diminishes the effect of cholesterol on the frequency and the bandwidth of the C-H stretching, CH2 scissoring and C=O stretching bands in FTIR spectra and the turbidity measurements (recorded as absorbance values at 440 nm) in pho...

Citation Formats

M. İlgü, R. M. Yennamalli, M. H. Lamm, T. Z. Sen, and M. Nilsen-Hamilton, “An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures,” RNA, pp. 815–824, 2014, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/46314.