TY - JOUR

T1 - Structure and hybridization properties of phosphoryl guanidine oligonucleotides under crowding conditions

AU - Kanarskaya, Maria A.

AU - Golyshev, Victor M.

AU - Pyshnyi, Dmitrii V.

AU - Lomzov, Alexander A.

N1 - Funding Information: V.M.G. acknowledges financial support from Russian Foundation for Basic Research project number 19-34-90127. M.A.K., D.V.P. and A.A.L. Russian State Federal budget project of ICBFM SB RAS [project number 0245-2021-0007] for the ON synthesis and data analysis.Victor Golyshev reports financial support, administrative support, equipment, drugs, or supplies, statistical analysis, and writing assistance were provided by Russian Foundation for Basic Research. Marya Kanarskaya, Dmitrii Pyshnyi, Alexander Lomzov reports financial support, administrative support, equipment, drugs, or supplies, and writing assistance were provided by Institute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences. Victor Golyshev reports a relationship with Russian Foundation for Basic Research that includes: employment, equity or stocks, funding grants, and non-financial support. Marya Kanarskaya, Dmitrii Pyshnyi and Alexander Lomzov reports a relationship with Institute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences that includes: consulting or advisory, employment, equity or stocks, non-financial support, and paid expert testimony. Dmitrii Pyshnyi has patent #US20170362270 pending to Licensee. D.V.P. is cofounders and shareholders of NOOGEN LLC, a company focused on the synthesis of PGO analogs. Funding Information: Victor Golyshev reports financial support, administrative support, equipment, drugs, or supplies, statistical analysis, and writing assistance were provided by Russian Foundation for Basic Research . Marya Kanarskaya, Dmitrii Pyshnyi, Alexander Lomzov reports financial support, administrative support, equipment, drugs, or supplies, and writing assistance were provided by Institute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences . Victor Golyshev reports a relationship with Russian Foundation for Basic Research that includes: employment, equity or stocks, funding grants, and non-financial support. Marya Kanarskaya, Dmitrii Pyshnyi and Alexander Lomzov reports a relationship with Institute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences that includes: consulting or advisory, employment, equity or stocks, non-financial support, and paid expert testimony. Dmitrii Pyshnyi has patent #US20170362270 pending to Licensee. D.V.P. is cofounders and shareholders of NOOGEN LLC , a company focused on the synthesis of PGO analogs. Funding Information: V.M.G. acknowledges financial support from Russian Foundation for Basic Research project number 19-34-90127 . M.A.K., D.V.P. and A.A.L. Russian State Federal budget project of ICBFM SB RAS [project number 0245-2021-0007 ] for the ON synthesis and data analysis. Publisher Copyright: © 2021 Elsevier Inc.

PY - 2021/11/5

Y1 - 2021/11/5

N2 - Phosphoryl guanidine oligonucleotides (PGOs) are promising uncharged analogs of nucleic acids and are used in a variety of applications. The importance of hydration is frequently ignored during the design of modified nucleic acid probes. Such hydrophobic modifications (phosphoryl guanidine) are expected to have a significant impact on the structure and thermal stability of the affected oligo with complementary nucleic acids. Here we aimed to investigate (by the osmotic stress method) hydration changes upon the formation of a duplex of a PGO with complementary DNA. According to our results, the presence of phosphoryl guanidines in one or both strands of a duplex only minimally affects hydration alterations under crowding conditions. The secondary structure of native and modified duplexes did not change significantly in the presence of ethanol, ethylene glycol, polyethylene glycol 200, or polyethylene glycol 1000. After the addition of a cosolvent, the thermodynamic stability of the PGO complexes changed in the same manner as that seen in a corresponding DNA duplex. The findings reported here and our previous studies form the basis for efficient use of PGOs in basic research and a variety of applications.

AB - Phosphoryl guanidine oligonucleotides (PGOs) are promising uncharged analogs of nucleic acids and are used in a variety of applications. The importance of hydration is frequently ignored during the design of modified nucleic acid probes. Such hydrophobic modifications (phosphoryl guanidine) are expected to have a significant impact on the structure and thermal stability of the affected oligo with complementary nucleic acids. Here we aimed to investigate (by the osmotic stress method) hydration changes upon the formation of a duplex of a PGO with complementary DNA. According to our results, the presence of phosphoryl guanidines in one or both strands of a duplex only minimally affects hydration alterations under crowding conditions. The secondary structure of native and modified duplexes did not change significantly in the presence of ethanol, ethylene glycol, polyethylene glycol 200, or polyethylene glycol 1000. After the addition of a cosolvent, the thermodynamic stability of the PGO complexes changed in the same manner as that seen in a corresponding DNA duplex. The findings reported here and our previous studies form the basis for efficient use of PGOs in basic research and a variety of applications.

KW - Molecular crowding

KW - Nucleic acid derivatives

KW - Phosphoryl guanidine oligonucleotides

KW - Solvation

KW - Thermodynamics

UR - http://www.scopus.com/inward/record.url?scp=85114666053&partnerID=8YFLogxK

U2 - 10.1016/j.bbrc.2021.09.001

DO - 10.1016/j.bbrc.2021.09.001

M3 - Article

C2 - 34509722

AN - SCOPUS:85114666053

VL - 577

SP - 110

EP - 115

JO - Biochemical and Biophysical Research Communications

JF - Biochemical and Biophysical Research Communications

SN - 0006-291X

ER -