HERMES – A software tool for prediction and analysis of magnetic field-induced residual dipolar couplings in nucleic acids

Ilektra-Chara Giassa^1,#, Andrea Vavřinská², Jiří Zelinka³, Jakub Sebera⁴, Vladimír Sychrovský⁴, Rolf Boelens², Radovan Fiala¹, Lukáš Trantírek^1*

¹ Central European Institute of Technology, Masaryk University, Brno, Czech Republic

² Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands

³ Faculty of Science, Masaryk University, Brno, Czech Republic

⁴ Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic

^*Corresponding author: lukas.trantirek@ceitec.muni.cz

HERMES is a web application for prediction of fiRDC and analysis of magnetic field induced RDC. fiRDC prediction is based on input 3D model structure(s) of nucleic acid (NA) fragment(s) [1] and built-in library of nucleic acid base specific magnetic susceptibility tensors and reference geometries [2]. When 3D model of NA is provided alongside experimental fiRDC, the program allows validation of the structure against calculated fiRDC data. When multiple models are provided, it allows identification of NA model(s) consistent with experimental fiRDC and/or quick assessment of nucleic acid fragment oligomeric state [3]. Additionally, the program built-in routine for rigid body modeling allows assessment of relative orientation of two domains in the nucleic acid structure. The program is written in MATLAB language and is executed on an Apache server interfaced with HTML, JavaScript and PHP. The web application and the source code in MATLAB are publically accessible at hermes.ceitec.muni.cz.

1. van Buuren BN, Schleucher J, Wittmann V, Griesinger C, Schwalbe H, Wijmenga SS (2004) NMR spectroscopic determination of the solution structure of a branched nucleic acid from residual dipolar couplings by using isotopically labeled nucleotides. Angew Chem Int Ed Engl, 43(2):187-92.

2. Vavřinská A, Zelinka J, Šebera J, Sychrovský V, Fiala R, Boelens R, Sklenář V, and Trantírek L (2016) Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin–spin interactions. J Biomol NMR, 64: 53–62.

3. Al-Hashimi H, Tolman J, Majumdar A, Gorin A, Patel D (2001) Determining Stoichiometry in Homomultimeric Nucleic Acid Complexes Using Magnetic Field Induced Residual Dipolar Couplings. J Am Chem Soc, 123, 5806-5807.