3′-MODIFIED OLIGO(2′-<i>O</i>-METHYLRIBONUCLEOTIDES) AS IMPROVED PROBES FOR HYBRIDIZATION WITH RNA

Новопашина, Д. С.; Totskaya, O. S.; Lomzov, Alexander A.; Venyaminova, Alya G.

doi:10.1081/ncn-200061795

Cited by 8 publications

(2 citation statements)

References 4 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…They are more resistant in biological media than natural RNA and form relatively stable complementary complexes with DNA and particularly with RNA, as well as triple helices with double-stranded DNA [246,247,248]. Coupling of thymidine nucleotide to 3'-terminus of the probe via “inverted” 3'-3'-phosphodiester bonds (Figure 19) stabilizes modified oligonucleotides against 3'-exonucleases [249,250,251]. Oligo(2'-O-methylribonucleotides) exhibit high rates of hybridization with nucleic acid targets, increased ability to bind structured RNA regions and to discriminate nucleotide mismatches in duplexes with RNA and DNA [252].…”

Section: Probes For Rna and Single-stranded Dna Imaging By Fluoresmentioning

confidence: 99%

Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells

et al. 2013

View full text Add to dashboard Cite

This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, OPEN ACCESSMolecules 2013, 18 15358 molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.

show abstract

Section: Probes For Rna and Single-stranded Dna Imaging By Fluoresmentioning

confidence: 99%

Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells

et al. 2013

View full text Add to dashboard Cite

show abstract

“…Besides, oligo(2′-O-methylribonucleotides) are remarkable for their increased ability to discriminate mismatches in comparison to oligodeoxyribonucleotides [ 14 ]. Additionally, we have modified the probes' 3′-termini by thymidine attached via a 3′-3′-phosphodiester internucleotide bond (3′-“inverted” thymidine) to achieve greater stability to exonucleases [ 15 – 17 ]. Previously we have reported the construction of tandems of two bis-pyrene conjugated oligo(2′-O-methylribonucleotides) as potential fluorescent SNP biosensors [ 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

Multipyrene Tandem Probes for Point Mutations Detection in DNA

Kholodar

Новопашина

Meschaninova

et al. 2013

Journal of Nucleic Acids

View full text Add to dashboard Cite

Here we report design, synthesis and characterization of highly sensitive, specific and stable in biological systems fluorescent probes for point mutation detection in DNA. The tandems of 3′- and 5′-mono- and bis-pyrene conjugated oligo(2′-O-methylribonucleotides), protected by 3′-“inverted” thymidine, were constructed and their potential as new instruments for genetic diagnostics was studied. Novel probes have been shown to exhibit an ability to form stable duplexes with DNA target due to the stabilizing effect of multiple pyrene units at the junction. The relationship between fluorescent properties of developed probes, the number of pyrene residues at the tandem junction, and the location of point mutation has been studied. On the basis of the data obtained, we have chosen the probes possessing the highest fluorescence intensity along with the best mismatch discrimination and deletion and insertion detection ability. Application of developed probes for detection of polymorphism C677T in MTHFR gene has been demonstrated on model systems.

show abstract

2′‐Bispyrene‐Modified 2′‐O‐Methyl RNA Probes as Useful Tools for the Detection of RNA: Synthesis, Fluorescent Properties, and Duplex Stability

et al. 2014

View full text Add to dashboard Cite

The synthesis and properties two series of new 2'-O-methyl RNA probes, each containing a single insertion of a 2'-bispyrenylmethylphosphorodiamidate derivative of a nucleotide (U, C, A, and G), are described. As demonstrated by UV melting studies, the probes form stable complexes with model RNAs and DNAs. Significant increases (up to 21-fold) in pyrene excimer fluorescence intensity were observed upon binding of most of the probes with complementary RNAs, but not with DNAs. The fluorescence spectra are independent of the nature of the modified nucleotides. The nucleotides on the 5'-side of the modified nucleotide have no effect on the fluorescence spectra, whereas the natures of the two nucleotides on the 3'-side are important: CC, CG, and UC dinucleotide units on the 3'-side of the modified nucleotide provide the maximum increases in excimer fluorescence intensity. This study suggests that these 2'-bispyrene-labeled 2'-O-methyl RNA probes might be useful tools for detection of RNAs.

show abstract

3′-MODIFIED OLIGO(2′-O-METHYLRIBONUCLEOTIDES) AS IMPROVED PROBES FOR HYBRIDIZATION WITH RNA

Cited by 8 publications

References 4 publications

Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells

Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells

Multipyrene Tandem Probes for Point Mutations Detection in DNA

2′‐Bispyrene‐Modified 2′‐O‐Methyl RNA Probes as Useful Tools for the Detection of RNA: Synthesis, Fluorescent Properties, and Duplex Stability

Contact Info

Product

Resources

About