Application of deuterium–hydrogen exchange to study the secondary structure of oligonucleotide ions in a gas phase


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Abstract

At present, the secondary structure of oligonucleotide ions in a gas phase is almost not understood. One of the main points is the retention of a hairpin secondary structure during ionization. In this work, we used a deuterium–hydrogen exchange reaction in a gas phase at atmospheric pressure for studying the conformational dynamics of oligonucleotide ions formed as a result of electrospray ionization. The exchange reactions of two oligonucleotides, which consisted of the identical sets of nucleotides but differed in their sequence, have been studied. One of these oligonucleotides formed a hairpin secondary structure, but the other did not. It has been found that both of the oligonucleotides demonstrate similar reaction dynamics of deuterium/hydrogen exchange in the gas phase; thereby indicating that the secondary structure has been completely destroyed during ionization.

About the authors

Yu. I. Kostyukevich

Skolkovo Institute of Science and Technology; Talrose Institute of Energy Problems of Chemical Physics; Moscow Institute of Physics and Technology (State University)

Author for correspondence.
Email: yura542@gmail.com
Russian Federation, Skolkovo, Moscow oblast, 143025; Moscow, 119334; Dolgoprudnyi, Moscow oblast, 141700

A. S. Kononikhin

Talrose Institute of Energy Problems of Chemical Physics; Moscow Institute of Physics and Technology (State University); Kulakov Research Center for Obstetrics, Gynecology, and Perinatology

Email: yura542@gmail.com
Russian Federation, Moscow, 119334; Dolgoprudnyi, Moscow oblast, 141700; Moscow, 117997

I. A. Popov

Emanuel Institute of Biochemical Physics; Moscow Institute of Physics and Technology (State University)

Email: yura542@gmail.com
Russian Federation, Moscow, 119334; Dolgoprudnyi, Moscow oblast, 141700

A. E. Bugrova

Emanuel Institute of Biochemical Physics; Kulakov Research Center for Obstetrics, Gynecology, and Perinatology

Email: yura542@gmail.com
Russian Federation, Moscow, 119334; Moscow, 117997

N. L. Starodubtseva

Moscow Institute of Physics and Technology (State University); Kulakov Research Center for Obstetrics, Gynecology, and Perinatology

Email: yura542@gmail.com
Russian Federation, Dolgoprudnyi, Moscow oblast, 141700; Moscow, 117997

E. N. Nikolaev

Skolkovo Institute of Science and Technology; Talrose Institute of Energy Problems of Chemical Physics; Moscow Institute of Physics and Technology (State University)

Email: yura542@gmail.com
Russian Federation, Skolkovo, Moscow oblast, 143025; Moscow, 119334; Dolgoprudnyi, Moscow oblast, 141700

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