Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State

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Yan, Shuting
Ilgu, Muslum
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American Chemical Society
Nilsen-Hamilton, Marit
University Professor
Lamm, Monica
Associate Professor
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Chemical and Biological Engineering

The function of the Department of Chemical and Biological Engineering has been to prepare students for the study and application of chemistry in industry. This focus has included preparation for employment in various industries as well as the development, design, and operation of equipment and processes within industry.Through the CBE Department, Iowa State University is nationally recognized for its initiatives in bioinformatics, biomaterials, bioproducts, metabolic/tissue engineering, multiphase computational fluid dynamics, advanced polymeric materials and nanostructured materials.

The Department of Chemical Engineering was founded in 1913 under the Department of Physics and Illuminating Engineering. From 1915 to 1931 it was jointly administered by the Divisions of Industrial Science and Engineering, and from 1931 onward it has been under the Division/College of Engineering. In 1928 it merged with Mining Engineering, and from 1973–1979 it merged with Nuclear Engineering. It became Chemical and Biological Engineering in 2005.

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1913 - present

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  • Department of Chemical Engineering (1913–1928)
  • Department of Chemical and Mining Engineering (1928–1957)
  • Department of Chemical Engineering (1957–1973, 1979–2005)
    • Department of Chemical and Biological Engineering (2005–present)

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Ames National Laboratory

Ames National Laboratory is a government-owned, contractor-operated national laboratory of the U.S. Department of Energy (DOE), operated by and located on the campus of Iowa State University in Ames, Iowa.

For more than 70 years, the Ames National Laboratory has successfully partnered with Iowa State University, and is unique among the 17 DOE laboratories in that it is physically located on the campus of a major research university. Many of the scientists and administrators at the Laboratory also hold faculty positions at the University and the Laboratory has access to both undergraduate and graduate student talent.

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Bioeconomy Institute
The Bioeconomy Institute at Iowa State University leads the nation and world in establishing the bioeconomy, where society obtains renewable fuel, energy, chemicals, and materials from agricultural sources. The institute seeks to advance the use of biorenewable resources for the production of fuels, energy, chemicals, and materials. The Institute will assure Iowa’s prominence in the revolution that is changing the way society obtains its essential sources of energy and carbon. This revolution will dramatically reduce our dependence on petroleum. Instead of fossil sources of carbon and energy, the bioeconomy will use biomass (including lignocellulose, starches, oils and proteins) as a renewable resource to sustain economic growth and prosperity. Agriculture will supply renewable energy and carbon to the bioeconomy while engineering will transform these resources into transportation fuels, commodity chemicals, and electric power. This transformation, however, must be done in a manner that meets our present needs without compromising those of future generations.
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Biochemistry, Biophysics and Molecular Biology

The Department of Biochemistry, Biophysics, and Molecular Biology was founded to give students an understanding of life principles through the understanding of chemical and physical principles. Among these principles are frontiers of biotechnology such as metabolic networking, the structure of hormones and proteins, genomics, and the like.

The Department of Biochemistry and Biophysics was founded in 1959, and was administered by the College of Sciences and Humanities (later, College of Liberal Arts & Sciences). In 1979 it became co-administered by the Department of Agriculture (later, College of Agriculture and Life Sciences). In 1998 its name changed to the Department of Biochemistry, Biophysics, and Molecular Biology.

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  • Department of Biochemistry and Biophysics (1959–1998)

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RNA aptamers are single-stranded oligonucleotides that bind to specific molecular targets with high affinity and specificity. To design aptamers for new applications, it is critical to understand the ligand binding mechanism in terms of the structure and dynamics of the ligand-bound and apo states. The problem is that most of the NMR or X-ray crystal structures available for RNA aptamers are for ligand-bound states. Available apo state structures, mostly characterized by crystallization under nonphysiological conditions or probed by low resolution techniques, might fail to represent the diverse structural variations of the apo state in solution. Here, we develop an approach to obtain a representative ensemble of apo structures that are based on in silico RNA 3D structure prediction and in vitro experiments that characterize base stacking. Using the neomycin-B aptamer as a case study, an ensemble of structures for the aptamer in the apo (unbound) state are validated and then used to investigate the ligand-binding mechanism for the aptamer in complex with neomycin-B.
This article is published as Yan, Shuting, Muslum Ilgu, Marit Nilsen-Hamilton, and Monica H. Lamm. "Computational Modeling of RNA Aptamers: Structure Prediction of the Apo State." The Journal of Physical Chemistry B 126, no. 37 (2022): 7114-7125. doi:10.1021/acs.jpcb.2c04649. Copyright © 2022 The Authors. This publication is licensed under CC-BY-NC-ND 4.0.