Analysis of new charge-neutral DNA/RNA analogues phosphoryl guanidine oligonucleotides (PGO) by gel electrophoresis

Alesya Fokina; Meiling Wang; Anna Ilyina; Kristina Klabenkova; Ekaterina Burakova; Boris Chelobanov; Dmitry Stetsenko

doi:10.1016/j.ab.2018.05.027

Analysis of new charge-neutral DNA/RNA analogues phosphoryl guanidine oligonucleotides (PGO) by gel electrophoresis

Anal Biochem. 2018 Aug 15:555:9-11. doi: 10.1016/j.ab.2018.05.027. Epub 2018 Jun 2.

Authors

Alesya Fokina¹, Meiling Wang², Anna Ilyina², Kristina Klabenkova², Ekaterina Burakova³, Boris Chelobanov⁴, Dmitry Stetsenko³

Affiliations

¹ Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia. Electronic address: fokina@niboch.nsc.ru.
² Novosibirsk State University, Novosibirsk, Russia.
³ Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.
⁴ Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.

PMID: 29864402
DOI: 10.1016/j.ab.2018.05.027

Abstract

Analysis and isolation of new charge-neutral phosphoryl guanidine oligonucleotides (PGO) by vertical slab electrophoresis were tested at different pH values (3-11) or in the presence of SDS as a micelle-forming agent. The most convenient way to analyze and purify phosphoryl guanidine oligonucleotides was by denaturing PAGE (8 M urea) at pH 3. The mobility of PGO is dependent on their A + C content. To analyze PGO containing only G, T or U, denaturing PAGE at pH 11 can be used, although the conditions need to be optimized. Bands were visualized by UV shadowing or Coomassie Brilliant Blue staining.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA / analysis*
Electrophoresis, Polyacrylamide Gel*
Guanidine / chemistry*
Oligonucleotides / analysis*
RNA / analysis*

Substances

Oligonucleotides
RNA
DNA
Guanidine