Home About us Contact | |||
Phosphoramidite Building Block (phosphoramidite + building_block)
Selected AbstractsScreening the Structural Space of Bicyclo-DNA: Synthesis and Thermal Melting Properties of bc4,3 -DNAEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 8 2009Andrea Stauffiger Abstract In attempts to screen the structural and functional properties of bicyclo-DNA, in which the ribose C(3,) and C(5,) centers are integrated into an additional five-membered carbocyclic ring ([3.3.0]-series) we have now synthesized and investigated a ring enlarged analogue in which C(5,) and C(3,) are spanned by a six-membered carbocyclic ring ([4.3.0]-series). The synthesis of the corresponding bc4,3 -T nucleoside 13 was performed in 12 steps by starting from known allyl furanose 1. X-ray analysis of its benzyl protected precursor 12 showed the cyclohexane ring to adopt a chair conformation with the O(5,) substituent in an axial position. The furanose part shows clearly S-type sugar pucker. This nucleoside was converted into the corresponding phosphoramidite building block 15 and incorporated into oligodeoxynucleotides by standard phosphoramidite chemistry. The thermal stabilities of oligonucleotides with single or double incorporations of bc4,3 -T residues, paired to complementary DNA or RNA, were found to be similar to those of unmodified oligonucleotides (,2.3 to +0.7 °C per modification) and to those with the known bc-T modifications. We also found that mismatch discrimination in the bc4,3 -T series was similar to that of the natural series but less discriminative in comparison to the known bc-T series.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Chemical Approach for the Study of the ,Kissing Complex' of Moloney murine leukaemia VirusHELVETICA CHIMICA ACTA, Issue 7 2008Sébastien Porcher Abstract The replication of Moloney murine leukaemia virus relies on the formation of a stable homodimeric ,kissing complex' of a GACG tetraloop interacting through only two C,G base pairs flanked of 5,-adjacent unpaired adenosines A9. Previous NMR investigations of a model stem loop 1 has not permitted to reveal the origin of this interaction. Therefore, with the aim of deeper comprehension of the phenomena, the model sequence 10 was prepared where position 9 has been substituted for a nucleoside offering a wider , -stacking. In this context, the wyosine phosphoramidite building block 2 was prepared and incorporated by adapting the conditions of the automated synthesis and developing original templated enzymatic ligation. However, no ,kissing interaction' has been observed for this model sequence 10 due to steric hindrance as confirmed by computational simulation. Consequently, several other model sequences, 18, 23,26, containing modified nucleosides were prepared. Finally, the importance of the cross-loop H-bond between G8 and G11 nucleobases was revealed by preparing a 18mer RNA hairpin 27, where the guanosine G8 has been substituted for inosine. The latter, which does not possess a C3 amino function compared to guanosine, is unable to form any ,kissing complex' demonstrating the importance of this secondary interaction in the formation of the complex. [source] Screening the Structural and Functional Properties of Bicyclo-DNA: bcox -DNACHEMBIOCHEM, Issue 14 2008Samuel Luisier Abstract The synthesis of two novel pyrimidine bicyclonucleosides (bcox -nucleosides) has been accomplished. These bicyclonucleosides each carry a lipophilic benzyloxime substituent on the carbocyclic ring and show improved conformational similarity to 2,-deoxyribonucleosides as shown by their X-ray structures. The thymine-containing bcox -nucleoside was converted into the corresponding phosphoramidite building block and incorporated into oligodeoxyribonucleotides by standard phosphoramidite chemistry. Tm data with complementary RNA and DNA were measured and compared to corresponding cases of natural and unfunctionalized bc-DNA. It was found that single incorporations of bcox residues destabilize duplexes by roughly 5,°C per modification. The destabilization was found to be due to the oxime substituent and not to the bicyclic scaffold itself. No significant alteration of the base-pairing selectivity as a function of the modification was observed. With RNA (but not with DNA) as a complement the relative thermal destabilization of bcox -oligothymidylates was gradually reduced and converted into a stabilizing interaction with increasing numbers of consecutive modifications. While no cellular uptake of bcox -oligonucleotides into HeLa cells occurred without transfecting agents, a significant increase in the transfection rate relative to unmodified DNA was observed in complexation with lipofectamine. [source] Pyrrolidino DNA with Bases Corresponding to the 2-Oxo Deletion Mutants of Thymine and Cytosine: Synthesis and Triplex-Forming PropertiesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2007Alain Mayer Abstract The dual recognition properties of pyrrolidino DNA species as parallel triplex-forming oligonucleotides were previously found to be strongly dependent upon the nature of the pyrimidine bases. In the structure,activity study presented here we were able to exclude this differential binding being due to their 2-oxo function. We had previously reported on the incorporation of pyrrolidino C -nucleosides into triplex-forming 2,-deoxyoligonucleotides (TFOs). The basic nitrogen atom that replaces the 4,-oxygen atom of the 2,-deoxysugar in such modified units introduces a positive charge in the third strand, and this is able to produce favourable electrostatic interaction with the negatively charged DNA target duplex. A first series of pyrrolidino pseudonucleosides with the bases isocytosine and uracil proved successful for GC base-pair recognition, but was unsuccessful for AT base-pair recognition within the parallel triplex binding motif. Here we report on the synthesis of the two novel 2,-deoxypyrrolidino nucleosides carrying the bases pyridin-2-one and 2-aminopyridine, their phosphoramidite building blocks and theirincorporation into TFOs. Pyrrolidinylpyridin-2-one (dp2P) and -2-aminopyridine (dp2AP), prepared as part of a structure,activity profiling of pyrrolidino DNA in triplex binding, are deletion mutants of T and C, respectively. We found by Tm measurements that neither modification increased triplex binding efficiency relative to the iso-C- and -U-containing pyrrolidino TFOs. These experiments clearly show that the C4 carbonyl function, although important for triplex binding through indirect contributions in general, is not responsible for the differential binding of the latter two aminonucleosides and suggest that TFO conformation is more important. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] pH-Independent Recognition of the dG,,,dC Base Pair in Triplex DNA: 9-Deazaguanine N7 -(2,-Deoxyribonucleoside) and Halogenated Derivatives Replacing Protonated dCHELVETICA CHIMICA ACTA, Issue 4 2006Frank Seela Abstract Triplex-forming oligonucleotides (TFOs) containing 9-deazaguanine N7 -(2,-deoxyribonucleoside) 1a and halogenated derivatives 1b,c were synthesized employing solid-phase oligonucleotide synthesis. For that purpose, the phosphoramidite building blocks 5a,c and 8a,c were synthesized. Multiple incorporations of 1a,c in place of dC were performed within TFOs, which involved the sequence of five consecutive 1a,c,,,dG,,,dC triplets as well as of three alternating 1a,c,,,dG,,,dC and dT,,,dA,,,dT triplets. These TFOs were designed to bind in a parallel orientation to the target duplex. Triplex forming properties of these oligonucleotides containing 1a,c in the presence of Na+ and Mg2+ were studied by UV/melting-curve analysis and confirmed by circular-dichroism (CD) spectroscopy. The oligonucleotides containing 1a in the place of dC formed stable triplexes at physiological pH in the case of sequence of five consecutive 1a,,,dG,,,dC triplets as well as three alternating 1a,c,,,dG,,,dC and dT,,,dA,,,dT triplets. The replacement of 1a by 9-halogenated derivatives 1b,c further enhanced the stability of DNA triplexes. Nucleosides 1a,c also stabilized duplex DNA. [source] |