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Intercalating Nucleic Acid (intercalating + nucleic_acid)

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Chemistry100%

Selected Abstracts

Twisted Intercalating Nucleic Acids , Intercalator Influence on Parallel Triplex Stabilities

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 17 2006
Vyacheslav V. Filichev
Abstract Phosphoramidites of several new twisted intercalating nucleic acid (TINA) monomers and the previously discovered (R)-1- O -[4-(1-pyrenylethynyl)phenylmethyl]glycerol (1) were synthesized and used in DNA synthesis. Stabilization of Hoogsteen-type triplexes was observed in cases of insertion of the novel (R)-1- O -[3-(naphthalen-1-ylethynyl)phenylmethyl]glycerol (2) as a bulge into homopyrimidine oligodeoxynucleotides (ONs), whereas phenylethynyl and 4-(biphenylylethynyl) derivatives of TINAs resulted in destabilization of parallel triplexes relative to the wild-type triplex. It was concluded that TINA monomers should possess at least two fused phenyl rings attached through the triple bond at the 4-position of bulged (R)-1- O -(phenylmethyl)glycerol in homopyrimidine ONs in order to stabilize parallel triplexes. Slight destabilization of DNA/DNA Watson,Crick type duplexes (,Tm = 1.0,4.5 °C) was detected for 2 inserted as a bulge, while RNA/DNA duplexes and duplexes with other TINA analogues were considerably destabilized (,Tm > 6.0 °C). In cases of double insertion of 1 opposite to base inversions in dsDNA, the thermal stabilities of the triplexes were higher than that of the wild-type triplex, which is a new solution to overcome the problem of targeting homopurine stretches with single base pair inversions. A DNA three-way junction was considerably stabilized (,Tm in a range of 10.0,15.5 °C) upon insertion of TINA monomers in the junction point as a bulge. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]

Stability of Hoogsteen -Type Triplexes , Electrostatic Attraction between Duplex Backbone and Triplex-Forming Oligonucleotide (TFO) Using an Intercalating Conjugate

HELVETICA CHIMICA ACTA, Issue 5 2008
Daniel Globisch
Abstract Syntheses are described for two novel twisted intercalating nucleic acid (TINA) monomers where the intercalator comprises a benzene ring linked to a naphthalimide moiety via an ethynediyl bridge. The intercalators Y and Z have a 2-(dimethylamino)ethyl and a methyl residue on the naphthalimide moiety, respectively. When used as triplex-forming oligonucleotides (TFOs), the novel naphthalimide TINAs show extraordinary high thermal stability in Hoogsteen -type triplexes and duplexes with high discrimination of mismatch strands. DNA Strands containing the intercalator Y show higher thermal triplex stability than DNA strands containing the intercalator Z. This observation can be explained by the ionic interaction of the protonated dimethylamino group under physiological conditions, targeting the negatively charged phosphate backbone of the duplex. This interaction leads to an extra binding mode between the TFO and the duplex, in agreement with molecular-modeling studies. We believe that this is the first example of an intercalator linking the TFO to the phosphate backbone of the duplex by an ionic interaction, which is a promising tool to achieve a higher triplex stability. [source]

Intercalating Nucleic Acids Containing Insertions of Naphthalimide

HELVETICA CHIMICA ACTA, Issue 9 2006
Michael
Abstract In a study of linker-length dependence, we evaluated naphthalimide (=,1H -benzo[de]isoquinoline-1,3(2H)-dione) and 4-bromonaphthalimide as intercalating nucleic acids. We used a vicinal dihydroxy system when incorporating the six different naphthalimide monomers into DNA, and found the minimum linker-length to be five C-atoms. With this length of the linker, naphthalimide was discriminating between DNA and RNA , stabilizing DNA, while destabilizing RNA. Furthermore, naphthalimide showed universal base character by hybridizing to the four natural bases with a range as narrow as 1.4°. When compared to pyrene, naphthalimide with the same linker-length gave significantly higher thermal meltings when hybridized to DNA. [source]