TY - JOUR

T1 - Diastereomers of a mono-substituted phosphoryl guanidine trideoxyribonucleotide

T2 - Isolation and properties

AU - Lomzov, Alexander A.

AU - Kupryushkin, Maxim S.

AU - Shernyukov, Andrey V.

AU - Nekrasov, Mikhail D.

AU - Dovydenko, Ilya S.

AU - Stetsenko, Dmitry A.

AU - Pyshnyi, Dmitrii V.

N1 - Publisher Copyright: © 2019 Elsevier Inc.

PY - 2019/6/11

Y1 - 2019/6/11

N2 - Recently, a new type of nucleic acid analogues with modified phosphate group, namely, phosphoryl guanidine oligonucleotides, has been described. In the present work, we assess the difference between diastereomers of a mono-substituted phosphoryl guanidine oligonucleotide and analyze their resistance to nuclease digestion. Individual diastereomers (‘fast’ and ‘slow’) of a trideoxynucleotide d (TpCp*A) were isolated by reverse-phase HPLC. Snake venom phosphodiesterase digestion showed that the native trideoxynucleotide was fully degraded after 30 min, whereas both ‘fast’ and ‘slow’ diastereomers of d (TpCp*A) were not completely digested even after 7 days. UV and CD spectra revealed similarities in the structure of the diastereomers. Structural analysis by 1D and 2D NMR spectroscopy also uncovered significant similarity in the properties of Rp and Sp diastereomers. Structural analysis of nuclear Overhauser effect spectroscopy (NOESY) data and restrained molecular dynamics methods showed very flexible single-stranded oligonucleotide structures. Detailed computational analysis of restraint penalty energies via restrained molecular dynamics simulations with the 2D NMR interproton distance data allowed us to conclude that most likely, the ‘fast’ isomer is the Sp diastereomer, and the ‘slow’ isomer is the Rp diastereomer.

AB - Recently, a new type of nucleic acid analogues with modified phosphate group, namely, phosphoryl guanidine oligonucleotides, has been described. In the present work, we assess the difference between diastereomers of a mono-substituted phosphoryl guanidine oligonucleotide and analyze their resistance to nuclease digestion. Individual diastereomers (‘fast’ and ‘slow’) of a trideoxynucleotide d (TpCp*A) were isolated by reverse-phase HPLC. Snake venom phosphodiesterase digestion showed that the native trideoxynucleotide was fully degraded after 30 min, whereas both ‘fast’ and ‘slow’ diastereomers of d (TpCp*A) were not completely digested even after 7 days. UV and CD spectra revealed similarities in the structure of the diastereomers. Structural analysis by 1D and 2D NMR spectroscopy also uncovered significant similarity in the properties of Rp and Sp diastereomers. Structural analysis of nuclear Overhauser effect spectroscopy (NOESY) data and restrained molecular dynamics methods showed very flexible single-stranded oligonucleotide structures. Detailed computational analysis of restraint penalty energies via restrained molecular dynamics simulations with the 2D NMR interproton distance data allowed us to conclude that most likely, the ‘fast’ isomer is the Sp diastereomer, and the ‘slow’ isomer is the Rp diastereomer.

KW - Diastereomer assignment

KW - Phosphodiesterase digestion assay

KW - Phosphoryl guanidine oligonucleotide

KW - Spatial structure

KW - ANALOGS

KW - DNA

KW - BACKBONE

KW - OLIGONUCLEOTIDES

UR - http://www.scopus.com/inward/record.url?scp=85064217496&partnerID=8YFLogxK

U2 - 10.1016/j.bbrc.2019.04.024

DO - 10.1016/j.bbrc.2019.04.024

M3 - Article

C2 - 31000201

AN - SCOPUS:85064217496

VL - 513

SP - 807

EP - 811

JO - Biochemical and Biophysical Research Communications

JF - Biochemical and Biophysical Research Communications

SN - 0006-291X

IS - 4

ER -