Evidence from CD spectra and melting temperatures for stable Hoogsteen-paired oligomer duplexes derived from DNA and hybrid triplexes

Efficient synthesis of the deoxysugar part of versipelostatin (VST) was achieved by direct and stereoselective glycosylation of the reduced VST aglycon. Activation of 2-deoxyglycosyl imidate with IBr under basic conditions enables alpha-selective glycosylation of beta-2-deoxylglycosides without anomerization. Comparison of the synthetic and natural VST products using NMR indicates that versipelostatin has a beta-D-digitoxose-(1,4)-alpha-L-oleandrose-(1,4)-beta-D-digitoxose trisaccharide. In addition, results of a biological assay indicate that the deoxyoligosaccharide unit of the synthetic glycoside was important for biological activity of the compound.

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“…As expected, the triplex with RNA as third strand is of higher thermal stability than that with DNA 18. 20…”

Section: Resultssupporting

confidence: 68%

Efficient Synthesis of the Deoxysugar Part of Versipelostatin by Direct and Stereoselective Glycosylation and Revision of the Structure of the Trisaccharide Unit

Tanaka

Yoshizawa

Chijiwa

et al. 2009

Chemistry An Asian Journal

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“…Moreover, the shift in peak position does not take place at ∼218 and ∼282 nm (see the Supporting Information). This implies that the triplex would be formed by a one-step docking under acidic conditions (55). At high pH, the CD spectra have no negative peak at ∼218 nm and present a typical characteristic of Watson-Crick duplex formation along with the temperature change (see the Supporting Information), which suggests that the triplex is not formed under this condition.…”

Section: Eigenpeak Of the CD Spectra For The Hoogsteen Pairedmentioning

confidence: 95%

pH and Cation Effects on the Properties of Parallel Pyrimidine Motif DNA Triplexes

et al. 2001

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The effects of cytosine protonation and various cations on the properties of parallel pyrimidine motif DNA triplexes were intensively investigated and characterized by several different techniques, such as circular dichroism (CD) conformation, ultraviolet (UV) melting, differential scanning calorimetry (DSC) thermal denaturation, and surface plasmon resonance (SPR) real-time dynamics. The comparative CD spectra of the triplex and the corresponding homoduplexes showed that the negative peak at approximately 218 nm would be the eigenpeak of the Hoogsteen paired strand, and moreover, the formation pathway of a triplex was significantly pH-dependent and fell into three groups: under acidic conditions, the triplex is formed by a one-step docking, under near physiological conditions, the Watson-Crick duplex is first structured and then accepts the Hoogsteen third strand into its major groove, and under basic conditions, the triplex is not formed. The pH-dependent thermodynamics of the global triplex, the Watson-Crick antiparallel duplex, and the Crick-Hoogsteen parallel duplex were comparatively discussed for the first time. These data revealed that the thermodynamic stabilities of the Watson-Crick-Hoogsteen triplex and the Crick-Hoogsteen duplex would be strongly dependent on cytosine protonation, but a low-pH environment somewhat destabilized the Watson-Crick duplex. The binding energy of triplex formation would be different from the unfolding energy of triplex melting under acidic conditions due to the disparity in the pathway between the formation and unfolding of a triplex. Real-time dynamic measurements showed that the association and dissociation rate constants of a duplex-to-triplex formation are (1.98 +/- 0.24) x 10(3) M(-1) s(-1) and (4.09 +/- 0.96) x 10(-4) s(-1) at 20 degrees C and pH 6.0, respectively. The formation energy of the duplex-to-triplex transition derived from SPR measurements was in agreement with the unfolding energy of the free Hoogsteen paired duplex derived from UV measurements. The calorimetric enthalpies of the triplex-to-duplex-to-single transition were 39.3 and 75.3 kcal/mol under near physiological conditions (pH 7.0), respectively, which were underestimated relative to the van't Hoff enthalpies. In addition, the effects of various cations, ionic strength, mixed-valent cations, and the position of the C(+)xG.C triplets on the thermodynamics of the triplexes were addressed under near physiological conditions. The interaction of metal ions with the triplexes clearly depended on the type and ionic strength of the cations, and the efficiency with which the cations stabilized the global triplex was in the order Mg(2+) > Mn(2+) > Ca(2+) > Ba(2+) >> Na(+). These observations would be useful for the design of triplex-forming oligonucleotides for antigene drugs and therapeutic purposes.

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“…16 The behavior of more complicated systems such as a DNA-RNA hybrid duplex and triplex is also scrutinized. 17,18 It is interesting that the CD showed that the homodimers, as well as single stranded DNA, also form a helical structure through base stacking. 12 Because deformation of the helical structure will change the shape of the CD spectrum, the reduction of the value and shift of the peak clearly indicate the degree of structural reorientation of dC 10 .…”

Section: Probing Molecular Change With CDmentioning

confidence: 99%

Anomalously high cooperativity of oligodeoxycytidylic acid for luminescence resonance energy transfer to lanthanide ions

et al. 2002

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The luminescence of terbium(III) and europium(III) through luminescence resonance energy transfer from mononucleotides and oligodeoxynucleotides is examined. Among mononucleotides, dGMP gives the strongest luminescence of terbium(III), while dTMP and dCMP yield a luminescence intensity of europium(III) that is larger than the other two cases. In the homodeoxydecamers, decadeoxycytidylic acid (dC10) produces the highest intensity for both metals. The anomalously large cooperativity of dC10 is explained by the easiness of deformation of the helical structure to bind lanthanide ions, and a circular dichroism study supports this explanation.

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Evidence from CD spectra and melting temperatures for stable Hoogsteen-paired oligomer duplexes derived from DNA and hybrid triplexes

Cited by 27 publications

References 51 publications

Efficient Synthesis of the Deoxysugar Part of Versipelostatin by Direct and Stereoselective Glycosylation and Revision of the Structure of the Trisaccharide Unit

Efficient Synthesis of the Deoxysugar Part of Versipelostatin by Direct and Stereoselective Glycosylation and Revision of the Structure of the Trisaccharide Unit

pH and Cation Effects on the Properties of Parallel Pyrimidine Motif DNA Triplexes

Anomalously high cooperativity of oligodeoxycytidylic acid for luminescence resonance energy transfer to lanthanide ions

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