Intercalating nucleic acids: The inversion of the stereocenter in 1-O-(pyren-1-ylmethyl)glycerol from R to S. Thermal stability towards ssDNA, ssRNA and its own type of oligodeoxynucleotides

Filichev, Vyacheslav V.; Hilmy, K. M. H.; Christensen, Ulf Bech; Pedersen, Erik B.

doi:10.1016/j.tetlet.2004.04.124

Cited by 19 publications

(16 citation statements)

References 10 publications

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“…[5,19] This was also the case in this study. While destabilizing, the carbon analogue 1 gave a marginally higher thermal melting than is reported for INA.…”

Section: Thermal Melting Studiessupporting

confidence: 81%

“…However, the 3 Melting temperatures of duplexes where a natural nucleotide was replaced either with another natural nucleotide or with monomers 1-3. The melting temperature of 3 versus 3 was taken from the literature [5] 5 -AGCTTGXCTTGAG-3 3 -TCGAACYGAACTC-5 (3), the narrow range is 2.6 • C. Shifting the intercalator to the opposite strand resulted in a more narrow range. Not surprisingly, the highest T m is achieved when the intercalator is placed opposite a cytosine and the lowest T m when the intercalator is facing a guanosine.…”

Section: Thermal Melting Studiesmentioning

confidence: 99%

“…Previously we have examined the stereochemistry of INA, showing the R-isomer being better than the S-isomer. [5] We have also investigated Pyrene Intercalating Nucleic Acids the influence of the linker length, showing that a longer linker will decrease the stabilization of the duplex. [6] In this article, we present a carbon linker analogue 1 to INA (3) and an intercalating nucleic acid 2 having two pyrene residues attached via the same carbon linker ( Figure 1).…”

Section: Introductionmentioning

confidence: 99%

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Pyrene Intercalating Nucleic Acids With a Carbon Linker

Østergaard

Wamberg

Pedersen

2011

Nucleosides, Nucleotides and Nucleic Acids

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We have synthesized a carbon linker analogue of INA (oligonucleotides containing insertions of 1-O-(1-pyrenylmethyl)glycerol). Thermal stability studies showed an increase in melting temperature in favor of the carbon linker analogue. We also synthesized a carbon linker analogue with two pyrenes geminally attached. Fluorescence studies of this intercalating nucleic acid with the pyrene moieties inserted as a bulge showed formation of an excimer band. When a mismatch was introduced at the site of the intercalator, an excimer band was formed for the destabilized duplexes whereas an exciplex band was observed when the stability of the duplex was retained.

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“…[5,19] This was also the case in this study. While destabilizing, the carbon analogue 1 gave a marginally higher thermal melting than is reported for INA.…”

Section: Thermal Melting Studiessupporting

confidence: 81%

Section: Thermal Melting Studiesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Pyrene Intercalating Nucleic Acids With a Carbon Linker

Østergaard

Wamberg

Pedersen

2011

Nucleosides, Nucleotides and Nucleic Acids

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“…An analysis of the thermodynamic data indicates that INA contacting oligonucleotides may be used for differentiating DNA/RNA chains (Filichev et al, 2004). …”

Section: Acyclic Analogs With Nucleobases and Their Analogs With Intementioning

confidence: 99%

“…Thus, it was concluded that intercalating nucleic acids with bulge insertions of (R )-1-O-(pyren-1-ylmethyl)glycerol have higher affinity for complementary ssDNAs than insertions of (S )-1-O-(pyren-1-ylmethyl)glycerol (Christensen et al, 2002, Filichev et al, 2004.…”

Section: Acyclic Analogs With Nucleobases and Their Analogs With Intementioning

confidence: 99%

Non-nucleosidic analogs of nucleic acids

Brzezinska¹,

Adrych-Rożek²,

Jahnz‐Wechmann³

et al. 2012

bta

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This paper presents several analogs of nucleic acids, including their structure and selected physico-chemical properties, reported recently as being obtained from non-nucleosidic units connected via phosphorodiester bonds. These analogs are built from units that instead of sugar residues carry different diol structures functionalized either with natural nucleobases or with other ring systems of an aromatic character. Some interesting nonnucleosidic oligonucleotide analogs and their applications are described. Unlocked (UNA) and glycerol nucleic acids (GNA) are also described.

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Locked Nucleic Acids and Intercalating Nucleic Acids in the Design of Easily Denaturing Nucleic Acids: Thermal Stability Studies

et al. 2004

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Intercalating nucleic acids (INA(R)s) with insertions of (R)-1-O-(1-pyrenylmethyl)glycerol were hybridized with locked nucleic acids (LNAs). INA/LNA duplexes were found to be less stable than the corresponding DNA/LNA duplexes when the INA monomer was inserted as a bulge close to the LNA monomers in the opposite strand. This property was used to make "quenched" complements that possess LNA in hairpins and in duplexes and are consequently more accessible for targeting native DNA. The duplex between a fully modified 13-mer LNA sequence and a complementary INA with six pyrene residues inserted after every second base as a bulge was found to be very unstable (Tm=30.1 degrees C) in comparison with the unmodified double-stranded DNA (Tm=48.7 degrees C) and the corresponding duplexes of LNA/DNA (Tm=81.6 degrees C) and INA/DNA (Tm=66.4 degrees C). A thermal melting experiment of a mixture of an LNA hairpin, with five LNA nucleotides in the stem, and its complementary DNA sequence gave a transition with an extremely low increase in optical density (hyperchromicity). When two INA monomers were inserted into the stem of the LNA hairpin, the same experiment resulted in a significant hyperchromicity comparable with the one obtained for the corresponding DNA/DNA duplex.

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Intercalating nucleic acids: The inversion of the stereocenter in 1-O-(pyren-1-ylmethyl)glycerol from R to S. Thermal stability towards ssDNA, ssRNA and its own type of oligodeoxynucleotides

Cited by 19 publications

References 10 publications

Pyrene Intercalating Nucleic Acids With a Carbon Linker

Pyrene Intercalating Nucleic Acids With a Carbon Linker

Non-nucleosidic analogs of nucleic acids

Locked Nucleic Acids and Intercalating Nucleic Acids in the Design of Easily Denaturing Nucleic Acids: Thermal Stability Studies

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