Bridged Oligonucleotides with Smoothed Hybridization Properties as a Tool for Analysis of Nucleotide Sequences

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Bridged oligonucleotides that contain nonnucleotide inserts, i.e., diethylene glycol phosphate residues (DEG insert) have been studied. These oligonucleotide derivatives were shown to smooth the melting temperatures of their DNA duplexes of various nucleotide composition. The DEG insert has been shown to have almost no effect on the sequence specificity of modified oligonucleotides and regulate only their hybridization properties. It has been demonstrated that bridged oligonucleotides immobilized on microparticles can be successfully used to specifically and efficiently reveal DNA templates during the parallel solid-phase hybridization analysis. The use of bridged oligonucleotides along with DNA-dependent enzymes (Taq DNA polymerase and T4 DNA ligase) in this analysis has led to pronounced discrimination of wrong DNA molecules due to the covalent attachment of the label to the carrier, thus increasing the reliability of the hybridization analysis.

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The authors would like to thank V.V. Koval (Center of the Collective Use, ICBFM, SB RAS) for recording mass spectra of bridged oligonucleotides.


The design of bridged oligonucleotides was supported by the State project no. А-0309-2016-0004. The study of modified oligonucleotides in the presence of DNA-dependent enzymes was supported by the grant no. 18-14-00357 from the Russian Scientific Foundation.

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Correspondence to I. A. Pyshnaya.

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Translated by A. Levina

Abbreviations: ODN, oligonucleotide (“deoxyribo” and prefix “d” for oligodeoxyribonucleotides are omitted); DEG insert, diethylene glycol phosphate residue; NA, nucleic acid; RT PCR, reverse transcription polymerase chain reaction; ou, optical unit; PB, phosphate buffer; TBEV, tick-borne encephalitis virus; 5'-UTR, 5'-untranslated region of the hepatitis C virus (HCV) genome; BCIP, 5-bromo-4-chloro-3-indolyl phosphate disodium salt; NBT, nitrotetrazolium blue; Tm, melting temperature of NA/NA complex.

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Pyshnaya, I.A., Lomzov, A.A. & Pyshnyi, D.V. Bridged Oligonucleotides with Smoothed Hybridization Properties as a Tool for Analysis of Nucleotide Sequences. Russ J Bioorg Chem 45, 677–683 (2019).

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  • modified oligonucleotides
  • bridged oligonucleotides
  • nonnucleotide modifications
  • smoothing
  • hybridization properties
  • enzymatic labeling
  • melting temperature