Physicochemical Properties of the Phosphoryl Guanidine Oligodeoxyribonucleotide Analogs

Dyudeeva, E. S.; Kupryushkin, Maxim S.; Lomzov, Alexander A.; Pyshnaya, I. A.; Pyshnyi, D. V.

doi:10.1134/s1068162019060153

Cited by 17 publications

(19 citation statements)

References 18 publications

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“…Previous studies have shown that introduction of PG groups into DNA may induce slight changes in the duplex structure and that the thermodynamic effect of a given chain modification in the duplex is sequence-dependent. 9 We designed a series of pairs of native and fully PG-modified oligodeoxyribonucleotides with the lengths of 8, 10, and 12 nt (Table 1). These oligomers contain 62.5, 50, and 41.7% of G/ C base pairs for the analysis of influences of length and various nucleotide compositions on the structure and hybridization properties.…”

Section: ■ Resultsmentioning

confidence: 99%

“…PGOs, i.e., deoxyribooligonucleotides carrying 1,3-dimethylimidazolidine-2-imine groups on phosphate residues, were synthesized by the LLC NOOGENE company using a protocol described previously. 3,9,31 The oligonucleotides were isolated by reverse-phase high-pressure chromatography by means of an Agilent 1200 chromatograph (Agilent, United States) on a column (4.6 × 150 mm) packed with the Eclipse XDB-C18 sorbent (5 μm; Agilent, United States). Elution was performed in a linear gradient of acetonitrile (0−90%) in 0.02 M triethylammonium acetate for 30 min at a flow rate of 1.5 mL/min.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

“…5,7,8 It has been shown that an increasing number of modifications in PGO/DNA duplexes significantly attenuates the dependence of melting temperature on solution ionic strength. 6,9 These properties make DMI-containing oligonucleotides a promising tool for biological studies and for accomplishing a wide range of practical tasks such as biosensing, molecular diagnostics, and therapeutics. 5,6,8,10−12 Nonetheless, the use of PGOs will become effective when physicochemical and biological properties of these derivatives are well understood.…”

Section: ■ Introductionmentioning

confidence: 99%

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Effects of Phosphoryl Guanidine Modification of Phosphate Residues on the Structure and Hybridization of Oligodeoxyribonucleotides

2021

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Phosphoryl guanidine oligonucleotides (PGOs) are promising tools for biological research and development of biosensors and therapeutics. We performed structural and hybridization analyses of octa-, deca-, and dodecamers with all phosphate residues modified by 1,3-dimethylimidazolidine-2-imine moieties. Similarity of the B-form double helix between native and modified duplexes was noted. In PGO duplexes, we detected a decrease in the proportion of C2′-endo and an increased proportion of C1′-exo sugar conformations of the modified chain. Applicability of the two-state model to denaturation transition of all studied duplexes was proved for the first time. Sequence-dependent effects of this modification on hybridization properties were observed. The thermal stability of PGO complexes is almost native at 100 mM NaCl and slightly increases with decreasing ionic strength. An increase in water activity and dramatic changes in interaction with cations and in solvation of PGOs and their duplexes were noted, resulting in slight elevation of the melting temperature after an ionic-strength decrease from 1 M NaCl down to deionized water. Decreased binding of sodium ions and decreased water solvation were documented for PGOs and their duplexes. In contrast to DNA, the PGO duplex formation leads to a release of several cations. The water shell is significantly more disordered near PGOs and their complexes. Nevertheless, changes in solvation during the formation of native and PGO complexes are similar and indicate that it is possible to develop models for predictive calculations of the thermodynamic properties of phosphoryl guanidine oligomers. Our results may help devise an approach for the rational design of PGOs as novel improved molecular probes and tools for many modern methods involving oligonucleotides.

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Section: ■ Resultsmentioning

confidence: 99%

Section: ■ Materials and Methodsmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

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Effects of Phosphoryl Guanidine Modification of Phosphate Residues on the Structure and Hybridization of Oligodeoxyribonucleotides

2021

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“…PGOs, as previously demonstrated, can form a complementary complex in solutions with ultralow ionic strength (Kupryushkin et al, 2014;Dyudeeva et al, 2019); therefore, it was essential to compare the efficiency rates of the reversetranscription reactions involving native versus PG-containing primers in buffers with different ionic strengths. For this purpose, potassium chloride was completely removed from the "standard" buffer, and the concentration of magnesium chloride was reduced from 5 to 2 mM.…”

Section: Resultsmentioning

confidence: 99%

“…Partially modified P-alkyl phosphonate oligonucleotides and phosphoryl guanidine oligodeoxyribonucleotides (PGOs), in which the ribose moiety remains unchanged, are utilized as primers to distinguish the "wrong" complex during PCR (Li T.-L. et al, 2019;Chubarov et al, 2020). For PGOs, it has been demonstrated that they form complexes with complementary DNA or RNA in solutions with low ionic strength, and even in deionized water; thermal stability of these complexes is comparable to that of the native complex under conditions close to physiological (Kupryushkin et al, 2014;Dyudeeva et al, 2019). Moreover, it is reported that spatial structure of duplexes containing PGOs is virtually the same as the structure of the double helix of two native nucleic acids (Lomzov et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Phosphoryl guanidine oligonucleotides as primers for RNA-dependent DNA synthesis using murine leukemia virus reverse transcriptase

Dyudeeva

Pyshnaya

2022

Vestn. VOGiS

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Modern approaches to the detection and analysis of low-copy-number RNAs are often based on the use of RNA-dependent DNA polymerases, for example, in reverse-transcription PCR. The accuracy and efficiency of cDNA synthesis in the reverse-transcription reaction catalyzed by reverse transcriptase (RNA-dependent DNA polymerase) significantly affect the correctness of the results of PCR diagnostic assays and/or RNA sequencing. In this regard, many studies are focused on the optimization of the reverse-transcription reaction, including the search for more perfect primers necessary to obtain a full-length DNA copy of RNA under study. The best-known completely uncharged analogs of oligonucleotides – morpholine oligonucleotides and peptide nucleic acids – cannot be substrates for enzymes that process nucleic acids. The aim of this work was to conduct a pilot study of uncharged phosphoryl guanidine oligodeoxyribonucleotides (PGOs) as primers for mouse leukemia virus reverse transcriptase (MMLV H-). Specific features of elongation of partially and completely uncharged PGO primers were investigated. It was demonstrated that PGOs can be elongated efficiently, e.g., in the presence of a fragment of human ribosomal RNA having complex spatial structure. It was shown that the proportion (%) of abortive elongation products of a PGO primer depends on buffer ionic strength, nucleotide sequence of the primer, and the presence and location of phosphoryl guanidine groups in the primer. The results indicate the suitability of PGOs, including completely electroneutral ones, as primers for reverse-transcription PCR, thereby opening up new prospects for the creation of experimental models for the analysis of highly structured RNA.

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Structure and hybridization properties of phosphoryl guanidine oligonucleotides under crowding conditions

Kanarskaya

Golyshev

Pyshnyi

et al. 2021

Biochemical and Biophysical Research Communications

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Physicochemical Properties of the Phosphoryl Guanidine Oligodeoxyribonucleotide Analogs

Cited by 17 publications

References 18 publications

Effects of Phosphoryl Guanidine Modification of Phosphate Residues on the Structure and Hybridization of Oligodeoxyribonucleotides

Effects of Phosphoryl Guanidine Modification of Phosphate Residues on the Structure and Hybridization of Oligodeoxyribonucleotides

Phosphoryl guanidine oligonucleotides as primers for RNA-dependent DNA synthesis using murine leukemia virus reverse transcriptase

Structure and hybridization properties of phosphoryl guanidine oligonucleotides under crowding conditions

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