RESUMO
Synthesis of three pyrene-modified nucleosides was accomplished using the CuAAC reaction. Hereby, pyrene is attached either to the 5'-position of thymidine or to the 2'-position of 2'-deoxyuridine through triazolemethylene linkers, or to the 2'-position of 2'-deoxyuridine through a more rigid triazole linker. The three nucleosides were incorporated into oligonucleotides, and these were combined in different duplexes and other secondary structures, which were analyzed by thermal stability and fluorescence studies. The three monomers were found to have different impacts on the nucleic acid complexes. Hence, pyrene attached to the 5'-position shows a tendency for intercalation into the duplex as indicated by a general decrease in fluorescence intensity followed by an increase in duplex thermal stability. Pyrene attached to the 2'-position through a rigid triazole linker also shows a tendency for intercalation but with decrease in duplex stability, whereas the pyrene attached to the 2'-position through a triazolemethylene linker is primarily situated in the minor groove as indicated by an increase in fluorescence but here in most cases leading to increase in duplex stability. All three pyrene nucleotides lead to thermal stabilization of bulged duplexes and three-way junctions. In some cases when two pyrenes were introduced into the core of these complexes, the formation or disappearance of a fluorescence excimer band can be used to indicate the hybridization process. Hereby these oligonucleotides can act as specific recognition probes.
Assuntos
Nucleosídeos/síntese química , Nucleotídeos/síntese química , Oligonucleotídeos/química , Oligonucleotídeos/síntese química , Pirenos/química , Pirenos/síntese química , Pareamento de Bases , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Nucleosídeos/química , Nucleotídeos/químicaRESUMO
Four double-headed nucleosides were prepared by the CuAAC reaction. Hereby, a triazole-containing linker connects an additional thymine or adenine to the 2'-position of 2'-deoxyuridine, a thymine to the 5'-position of thymidine and a thymine to the 6'-position of an LNA-thymidine monomer. Whereas no conclusive recognition effects of the additional thymines were found when introduced in LNA or at the 5'-position, both thymine and adenine in the 2'-position were found to stabilise three-way junctions in both dsDNA and DNA : RNA contexts and to give cross-strand interactions in a DNA-duplex, when specifically introduced in a so-called (+1)-zipper motif.
Assuntos
Conformação de Ácido Nucleico , Ácidos Nucleicos/química , Nucleosídeos/síntese químicaRESUMO
Two bicyclic 2'-deoxynucleoside analogues are synthesized in 12 steps each from thymidine. With a six-membered ring fused to the C3'-C4' bond and an alpha-L-ribo- and a beta-D-xylo-configuration, these are conformationally restricted in an S- and an N-type conformation, respectively. The constitutions were proven by X-ray crystallography. The beta-D-xylo-configured analogue is successfully converted to a 3'-phosphoramidite and incorporated into oligodeoxynucleotides, which are found to hybridize to DNA and RNA complements with decreased affinity.
Assuntos
Compostos Bicíclicos Heterocíclicos com Pontes/síntese química , Nucleosídeos/síntese química , Ribose/química , Xilose/química , Sequência de Bases , Biomimética , Compostos Bicíclicos Heterocíclicos com Pontes/química , Configuração de Carboidratos , Cristalografia por Raios X , DNA/química , DNA/genética , DNA/metabolismo , Desnaturação de Ácido Nucleico , Nucleosídeos/química , Oligonucleotídeos/química , Oligonucleotídeos/genética , Oligonucleotídeos/metabolismo , RNA/química , RNA/genética , RNA/metabolismo , Estereoisomerismo , Especificidade por Substrato , Temperatura de TransiçãoRESUMO
Two series of thymidine derivatives with additional nucleobases/aromatics attached to either the 5'(S)-C- or the 5-position were prepared by epoxide opening and/or "click chemistry" cycloaddition protocols and introduced into DNA duplexes. Interstrand base-base communication in the minor groove and intrastrand stacking interactions in the major groove were detected.
Assuntos
DNA/química , Timidina/análogos & derivados , Conformação de Ácido Nucleico , Desnaturação de Ácido Nucleico , Nucleosídeos de Pirimidina/síntese química , Nucleosídeos de Pirimidina/química , Temperatura , Triazóis/químicaRESUMO
Oligonucleotides containing 7-deaza-2'-deoxyxanthosine (1) and 2'-deoxyxanthosine (2) were prepared. The 2-(4-nitrophenyl)ethyl group is applicable for 7-deazaxanthine protection that is removed with DBU by beta-elimination, while the deprotection of the allyl residue with Pd (0) catalyst failed. Contrarily, the allyl group was found to be an excellent protecting group for 2'-deoxyxanthosine (2). The base pairing of nucleosides 1 and 2 with the four canonical DNA constituents as well as with 3 within the 12-mer duplexes is studied.
Assuntos
Pareamento de Bases , Desoxirribonucleosídeos/química , Nucleosídeos/química , Oligonucleotídeos/química , Compostos Organofosforados/síntese química , Compostos Organofosforados/química , Temperatura de TransiçãoRESUMO
Triplex-forming oligonucleotides (TFOs) containing 2'-deoxyisoguanosine (2), 7-bromo-7-deaza-2'-deoxyisoguanosine (2) as well as the propynylated 9-deazaguanine N7-(2'-deoxyribonucleoside) were prepared. For this the phosphoramidites 9a, b of the nucleoside 1 and, the phosphoramidites 19, 20 of compound 3b were synthesized. They were employed in solid-phase oligonucleotide synthesis to yield the protected 31-mer oligonucleotides. The deblocking of the allyl-protected oligonucleotides containing 1 was carried out by Pd(0)[PPh3]4-PPh3 followed by 25% aq. NH3. Formation of the 31-mer single-stranded intramolecular triplexes was studied by UV-melting curve analysis. In the single-stranded 31-mer oligonucleotides the protonated dC in the dCH(+)-dG-dC base triad was replaced by 2'-deoxyisoguanosine (1), 7-bromo-7-deaza-2'-deoxyisoguanosine (2) and, 9-deaza-9-propynylguanine N7-(2'-deoxyribonucleoside) (3b). The replacement of protonated dC by compounds 1 and 3b resulted in intramolecular triplexes which are formed pH-independently and are stable under neutral conditions. These triplexes contain "purine" nucleosides in the third pyrimidine rich strand of the oligonucleotide hairpin.
Assuntos
Citosina/química , DNA/química , DNA/síntese química , Guanina/análogos & derivados , Conformação de Ácido Nucleico , Prótons , Sequência de Bases , Cromatografia Líquida de Alta Pressão , DNA/genética , Guanina/síntese química , Guanina/química , Concentração de Íons de Hidrogênio , Espectroscopia de Ressonância Magnética , Dados de Sequência Molecular , Peso Molecular , Oligonucleotídeos/síntese química , Oligonucleotídeos/química , Oligonucleotídeos/genética , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Temperatura de TransiçãoRESUMO
In the title compound, 2'-deoxy-7-propynyl-7-deazaadenosine, C14H16N4O3, the torsion angle of the N-glycosylic bond is anti [chi = -130.7 (2) degrees ]. The sugar pucker of the 2'-deoxyribofuranosyl moiety is C2'-endo-C3'-exo, 2T3 (S-type), with P = 185.9 (2) degrees and tau(m) = 39.1 (1) degrees , and the orientation of the exocyclic C4'-C5' bond is -ap (trans). The 7-substituted propynyl group is nearly coplanar with the heterocyclic base moiety. Molecules of the nucleoside form a layered network in which the heterocyclic bases are stacked head-to-tail with a closest distance of 3.197 (1) A. The crystal structure of the nucleoside is stabilized by three intermolecular hydrogen bonds of types N-H... O, O-H... N and O-H... O.
Assuntos
DNA/química , Desoxiadenosinas/química , Cristalografia por Raios X , Ligação de Hidrogênio , Estrutura MolecularRESUMO
The stabilizing effect of 7-propynylated 7-deazapurine nucleosides on DNA-hairpins and DNA-duplexes containing d(GA) mismatches was investigated. The corresponding oligonucleotides were synthesized using solid-phase synthesis. For this purpose, the phosphoramidite of 7-deaza-7-propynyl-2'-deoxyadenosine (3c) was prepared. The incorporation of 3c instead of dA into the tandem d(GA) base pair of a DNA-hairpin alters the secondary structure, but has a positive effect on the duplex stability. A complete replacement of the canonical nucleosides of the tandem d(GA) base pair by 3c and 7-deaza-7-propynyl-2'-deoxyguanosine results in a significant base pair stabilization.
Assuntos
Pareamento de Bases , Desoxiadenosinas/química , Desoxiguanosina/análogos & derivados , Sequência de Bases , Dicroísmo Circular , Desoxiguanosina/química , Conformação de Ácido Nucleico , TermodinâmicaRESUMO
Oligonucleotides containing 7-deazapurines or 9-deazapurines with propynyl groups at the 7- or 9-position were prepared. The stabilizing effect of the propynyl group was studied on DNA duplexes, hairpins and triplexes.
Assuntos
DNA/química , Ácidos Nucleicos Heteroduplexes/química , Purinas/química , Sequência de Bases , Modelos Químicos , Biologia Molecular/métodos , Dados de Sequência Molecular , Oligonucleotídeos/química , Oligonucleotídeos Antissenso/química , Compostos Organofosforados/química , Purinas/farmacologia , Temperatura , TermodinâmicaRESUMO
In the title compound, 2-amino-7-(2-deoxy-beta-D-erythro-pentofuranosyl)-3,7-dihydropyrrolo[2,3-d]pyrimidin-4-one, C11H14N4O4, the N-glycosylic bond torsion angle, chi, is anti [-106.5 (3) degrees ]. The 2'-deoxyribofuranosyl moiety adopts the 3T4 (N-type) conformation, with P = 39.1 degrees and tau(m) = 40.3 degrees . The conformation around the exocyclic C-C bond is ap (trans), with a torsion angle, gamma, of -173.8 (3) degrees . The nucleoside forms a hydrogen-bonded network, leading to a close-packed multiple-layer structure with a head-to-head arrangement of the bases. The nucleobase interplanar O=C-C...NH(2) distance is 3.441 (1) A.