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1.
The preparation and the pairing properties of the new 3′‐deoxyribopyranose (4′→2′)‐oligonucleotide (=p‐DNA) pairing system, based on 3′‐deoxy‐β‐D ‐ribopyranose nucleosides is presented. D ‐Xylose was efficiently converted to the prefunctionalized 3‐deoxyribopyranose derivative 4‐O‐[(tert‐butyl)dimethylsilyl]‐3‐deoxy‐D ‐ribopyranose 1,2‐diacetate 8 (obtained as a 4 : 1 mixture of α‐ and β‐D ‐anomers; Scheme 1). From this sugar building block, the corresponding, appropriately protected thymine, guanine, 5‐methylcytosine, and purine‐2,6‐diamine nucleoside phosphoramidites 29 – 32 were prepared in a minimal number of steps (Schemes 2–4). These building blocks were assembled on a DNA synthesizer, and the corresponding p‐DNA oligonucleotides were obtained in good yields after a one‐step deprotection under standard conditions, followed by HPLC purification (Scheme 5 and Table 1). Qualitatively, p‐DNA shows the same pairing behavior as p‐RNA, forming antiparallel, exclusively Watson‐Crick‐paired duplexes that are much stronger than corresponding DNA duplexes. Duplex stabilities within the three related (i.e., based on ribopyranose nucleosides) oligonucleotide systems p‐RNA, p‐DNA, and 3′‐O‐Me‐p‐RNA were compared with each other (Table 2). Intrinsically, p‐RNA forms the strongest duplexes, followed by p‐DNA, and 3′‐O‐Me‐p‐RNA. However, by introducing the nucleobases purine‐2,6‐diamine (D) and 5‐methylcytosine (M) instead of adenine and cytosine, a substantial increase in stability of corresponding p‐DNA duplexes was observed.  相似文献   

2.
The title compound, 2,4‐diamino‐5‐bromo‐7‐(2‐deoxy‐2‐fluoro‐β‐d ‐arabinofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine, C11H13BrFN5O3, shows two conformations of the exocyclic C4′—C5′ bond, with the torsion angle γ (O5′—C5′—C4′—C3′) being 170.1 (3)° for conformer 1 (occupancy 0.69) and 60.7 (7)° for conformer 2 (occupancy 0.31). The N‐glycosylic bond exhibits an anti conformation, with χ = −114.8 (4)°. The sugar pucker is N‐type (C3′‐endo; 3T4), with P = 23.3 (4)° and τm = 36.5 (2)°. The compound forms a three‐dimensional network that is stabilized by several intermolecular hydrogen bonds (N—H...O, O—H...N and N—H...Br).  相似文献   

3.
Oligonucleotides composed of 1′,5′‐anhydro‐arabino‐hexitol nucleosides belonging to the L series (L ‐HNA) were prepared and preliminarily studied as a novel potential base‐pairing system. Synthesis of enantiopure L ‐hexitol nucleotide monomers equipped with a 2′‐(N6‐benzoyladenin‐9‐yl) or a 2′‐(thymin‐1‐yl) moiety was carried out by a de novo approach based on a domino reaction as key step. The L oligonucleotide analogues were evaluated in duplex formation with natural complements as well as with unnatural sugar‐modified oligonucleotides. In many cases stable homo‐ and heterochiral associations were found. Besides Tm measurements, detection of heterochiral complexes was unambiguously confirmed by LC‐MS studies. Interestingly, circular dichroism measurements of the most stable duplexes suggested that L ‐HNA form left‐handed helices with both D and L oligonucleotides.  相似文献   

4.
Oligonucleotides containing halogenated `purine' and pyrimidine bases were synthesized. Bromo and iodo substituents were introduced at the 7‐position of 8‐aza‐7‐deazapurine‐2,6‐diamine (see 2b , c ) or at the 5‐position of uracil residues (see 3b , c ). Phosphoramidites were synthesized after protection of 2b with the isobutyryl residue and of 2c with the benzoyl group. Duplexes containing the residues 2b or 2c gave always higher Tm values than those of the nonmodified counterparts containing 2′‐deoxyadenosine, the purine‐2,6‐diamine 2′‐deoxyribonucleoside ( 1 ), or 2a at the same positions. Six 2b residues replacing dA in the duplex 5′‐d(TAGGTCAATACT)‐3′ ( 11 )⋅5′‐d(AGTATTGACCTA)‐3′ ( 12 ) raised the Tm value from 48 to 75° (4.5° per modification (Table 3)). Contrary to this, incorporation of the 5‐halogenated 2′‐deoxyuridines 3b or 3c into oligonucleotide duplexes showed very little influence on the thermal stability, regardless of which `purine' nucleoside was located opposite to them (Tables 4 and 5). The positive effects on the thermal stability of duplexes observed in DNA were also found in DNA⋅RNA hybrids or in DNA with parallel chain orientation (Tables 8 and 9, resp.).  相似文献   

5.
The 1,3,4,6‐tetra‐O‐acetyl‐2‐azido‐2‐deoxy‐β‐D ‐mannopyranose ( 4 ) or the mixture of 1,3,6‐tri‐O‐acetyl‐2‐azido‐2‐deoxy‐4‐O‐(2,3,4,6‐tetra‐O‐acetyl‐β‐D ‐galactopyranosyl)‐β‐D ‐mannopyranose ( 10 ) and the corresponding α‐D ‐glucopyranose‐type glycosyl donor 9 / 10 reacted at room temperature with protected nucleosides 12 – 15 in CH2Cl2 solution in the presence of BF3?OEt2 as promoter to give 5′‐O‐(2‐azido‐2‐deoxy‐α‐D ‐glycosyl)nucleosides in reasonable yields (Schemes 2 and 3). Only the 5′‐O‐(α‐D ‐mannopyranosyl)nucleosides were obtained. Compounds 21, 28, 30 , and 31 showed growth inhibition of HeLa cells and hepatoma Bel‐7402 cells at a concentration of 10 μM in vitro.  相似文献   

6.
Dipyrido[3,2-a:2′,3′-c]phenazine (dppz) derivatives were conjugated to 9-mer and 18-mer DNA (ODN) at a site without nucleobase, either at the 5′- or 3′-end or at a internucleotide position, via linkers of 7, 12, or 18 atoms lengths. These dppz-linked ODNs were synthesized using novel backbone glycerol phosphoramidites: Glycerol, serving as artificial nucleoside without nucleobase, was modified to amines 10 , 23 , and 24 , which were suitable for the subsequent key reaction with dppz-carboxylic acid 3 (Schemes 2 and 3). The products of these reactions (see 5 – 7 ) were then transformed to the standard phosphoramidite derivatives (see 27 , 29 , and 30 ) or used for loading on a CPG support (see 28 , 31 , and 32 ). The dppz-modified ODNs were subsequently assembled in the usual manner using automated solid-phase DNA synthesis. The 9-mer ODN-dppz conjugates 35 – 43 were tested for their ability to form stable duplexes with target DNA or RNA strands (D11 ( 60 ) or R11 ( 61 )), while the 18-mer ODN-dppz conjugates 48 – 56 were tested for their ability to form stable triplexes with a DNA target duplex D24⋅D24 ( 62 ) (see Tables 1 and 2). The presence of the conjugated dppz derivative increases the stability of DNA⋅DNA and DNA⋅RNA duplexes, typically by a ΔTm of 7.3 – 10.9° and 4.5 – 7.4°, respectively, when the dppz is tethered at the 5′- or 3′-terminal (Table 2). The dppz derivatives also stabilize triplexes when attached to the 5′- or 3′-end, with a ΔTm varying from 3.8 – 11.1° (Table 3). The insertion of a dppz building block at the center of a 9-mer results in a considerably poorer stability of the corresponding DNA⋅DNA duplexes (ΔTm=0.5 to 4.2°) and DNA⋅RNA duplexes (ΔTm=−1.5 to 0.9°), while the replacement of one interior nucleotide by a dppz building unit in the corresponding 8-mer ODN does not reveal the formation of any duplex at all. Different types of modifications in the middle of the 18-mer ODN, in general, do not lead to any triplex formation, except when the dppz derivative is tethered to the ODN through a 12-atom-long linker (Entry 9 in Table 3).  相似文献   

7.
The syntheses and the fluorescence properties of 7H‐3,6‐dihydro‐1,2,3‐triazolo[4,5‐d]pyrimidin‐7‐one 2′‐deoxy‐β‐D ‐ribonucleosides (=2′‐deoxy‐8‐azainosine) 3 (N3), 15 (N2), and 16 (N1) as well as of 1,2,3‐benzotriazole 2′‐O‐methyl‐β‐ or ‐α‐D ‐ribofuranosides 6 (N1) and 24 (N1) are described. Also the fluorescence properties of 1,2,3‐benzotriazole 2′‐deoxy‐β‐D ‐ribofuranosides 4 (N1) and 5 (N2) are evaluated. From the nucleosides 3 – 6 , the phosphoramidites 19, 26a, 26b , and 28 are prepared and employed in solid‐phase oligonucleotide synthesis. In 12‐mer DNA duplexes, compound 3 shows similar ambiguous base‐pairing properties as 2′‐deoxyinosine ( 1 ), while the nucleosides 4 – 6 show strong pairing with each other and discriminate very little the four canonical DNA constituents.  相似文献   

8.
Two modified DNA 14‐mers have been prepared, containing either a 2‐deoxy‐D ‐erythrose‐derived adenosine analogue carrying a C(8)−CH2O group (deA*), or a 2‐deoxy‐D ‐erythrose‐derived uridine analogue, possessing a C(6)−CH2O group (deU*). These nucleosides are linked via a phosphinato group between O−C(3′) (deA* and deU*) and O−C(5′) of one neighbouring nucleotide, and between C(8)−CH2O (deA*), or C(6)−CH2O (deU*) and O−C(3′) of the second neighbour. N6‐Benzoyl‐9‐(β‐D ‐erythrofuranosyl)adenine ( 3 ) and 1‐(β‐D ‐erythrofuranosyl)uracil ( 4 ) were prepared from D ‐glucose, deoxygenated at C(2′), and converted into the required phosphoramidites 1 and 2 . The modified tetradecamers 31 and 32 were prepared by solid‐phase synthesis. Pairing studies show a decrease in the melting temperature of 7 to 8 degrees for the duplexes 31 ⋅ 30 and 32 ⋅ 29 , as compared to the unmodified DNA duplex 29 ⋅ 30 . A comparison with the pairing properties of tetradecamers similarly incorporating deoxyribose‐ instead of the deoxyerythrose‐derived nucleotides evidences that the CH2OH substituent at C(4′) has no significant effect on the pairing.  相似文献   

9.
2,2′‐Anhydro‐1‐(3′,5′‐di‐O‐acetyl‐β‐D‐arabinofuranosyl)uracil, C13H14N2O7, was obtained by refluxing 2′,3′‐O‐(methoxymethylene)uridine in acetic anhydride. The structure exhibits a nearly perfect C4′‐endo (4E) conformation. The best four‐atom plane of the five‐membered furanose ring is O—C—C—C, involving the C atoms of the fused five‐membered oxazolidine ring, and the torsion angle is only −0.4 (2)°. The oxazolidine ring is essentially coplanar with the six‐membered uracil ring [r.m.s. deviation = 0.012 (5) Å and dihedral angle = −3.2 (3)°]. The conformation at the exocyclic C—C bond is gauche–trans which is stabilized by various C—H...π and C—O...π interactions.  相似文献   

10.
In the title compound [systematic name: 7‐(2‐de­oxy‐β‐d ‐erythro‐pentofuranos­yl)‐2‐fluoro‐7H‐pyrrolo[2,3‐d]pyrimidin‐2‐amine], C11H13FN4O3, the conformation of the N‐glycosylic bond is between anti and high‐anti [χ = −110.2 (3)°]. The 2′‐deoxy­ribofuranosyl unit adopts the N‐type sugar pucker (4T3), with P = 40.3° and τm = 39.2°. The orientation of the exocyclic C4′—C5′ bond is −ap (trans), with a torsion angle γ = −168.39 (18)°. The nucleobases are arranged head‐to‐head. The crystal structure is stabilized by four inter­molecular hydrogen bonds of types N—H⋯N, N—H⋯O and O—H⋯O.  相似文献   

11.
The automated on‐line synthesis of DNA‐3′‐PNA chimeras 1 – 4 and (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras 5 – 8 is described, in which the 3′‐terminal part of the oligonucleotide is linked to the N‐terminal part of the PNA via N‐(ω‐hydroxyalkyl)‐N‐[(thymin‐1‐yl)acetyl]glycine units (alkyl=Et, Ph, Bu, and pentyl). By means of UV thermal denaturation, the binding affinities of all chimeras were directly compared by determining their Tm values in the duplex with complementary DNA and RNA. All investigated DNA‐3′‐PNA chimeras and (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras form more‐stable duplexes with complementary DNA and RNA than the corresponding unmodified DNA. Interestingly, a N‐(3‐hydroxypropyl)glycine linker resulted in the highest binding affinity for DNA‐3′‐PNA chimeras, whereas the (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras showed optimal binding with the homologous N‐(4‐hydroxybutyl)glycine linker. The duplexes of (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras and RNA were significantly more stable than those containing the corresponding DNA‐3′‐PNA chimeras. Surprisingly, we found that the charged (2′‐O‐methyl‐RNA)‐3′‐PNA chimera with a N‐(4‐hydroxybutyl)glycine‐based unit at the junction to the PNA part shows the same binding affinity to RNA as uncharged PNA. Potential applications of (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras include their use as antisense agents acting by a RNase‐independent mechanism of action, a prerequisite for antisense‐oligonucleotide‐mediated correction of aberrant splicing of pre‐mRNA.  相似文献   

12.
In the title regioisomeric nucleosides, alternatively called 1‐(2‐deoxy‐β‐d ‐erythro‐furan­osyl)‐1H‐pyrazolo­[3,4‐d]­pyrimidine, C10H12N4O3, (II), and 2‐(2‐deoxy‐β‐d ‐erythro‐furan­osyl)‐2H‐pyrazolo­[3,4‐d]pyrimidine, C10H12N4O3, (III), the conformations of the gly­cosyl­ic bonds are anti [?100.4 (2)° for (II) and 15.0 (2)° for (III)]. Both nucleosides adopt an S‐type sugar pucker, which is C2′‐endo‐C3′‐exo (2T3) for (II) and 3′‐exo (between 3E and 4T3) for (III).  相似文献   

13.
The title compound [systematic name: 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐ethynylpyrimidin‐2(1H)‐one], C11H13N3O4, shows two conformations in the crystalline state. The N‐glycosylic bonds of both conformers adopt similar conformations, with χ = −149.2 (1)° for conformer (I‐1) and −151.4 (1)° for conformer (I‐2), both in the anti range. The sugar residue of (I‐1) shows a C2′‐endo envelope conformation (2E, S‐type), with P = 164.7 (1)° and τm = 36.9 (1)°, while (I‐2) shows a major C3′‐exo sugar pucker (C3′‐exo‐C2′‐endo, 3T2, S‐type), with P = 189.2 (1)° and τm = 33.3 (1)°. Both conformers participate in the formation of a layered three‐dimensional crystal structure with a chain‐like arrangement of the conformers. The ethynyl groups do not participate in hydrogen bonding, but are arranged in proximal positions.  相似文献   

14.
A general synthesis of the four isomeric N7α‐D ‐, N7β‐D ‐, N9α‐D ‐, and N9β‐D ‐(purin‐2‐amine deoxynucleoside phosphoramidite) building blocks for DNA synthesis is described (Scheme). The syntheses start with methyl 3′,5′‐di‐O‐acetyl‐2′‐deoxy‐D ‐ribofuranoside ( 2 ) as the sugar component and the N2‐acetyl‐protected 6‐chloropurin‐2‐amine 1 as the base precursor. N7‐Selectivity was achieved by kinetic control, and N9‐selectivity by thermodynamic control of the nucleosidation reaction. The two N7‐(purin‐2‐amine deoxynucleosides) were introduced into the center of a decamer DNA duplex, and their pairing preferences were analyzed by UV‐melting curves. Both the N7α‐D ‐ and N7β‐D ‐(purin‐2‐amine nucleotide) units preferentially pair with a guanine base within the Watson‐Crick pairing regime, with ΔTms of −6.7 and −8.7 K, respectively, relative to a C⋅G base pair (Fig. 3 and Table 1). Molecular modeling suggests that, in the former base pair, the purinamine base is rotated into the syn‐arrangement and is able to form three H‐bonds with O(6), N(1), and NH2 of guanine, whereas in the latter base pair, both bases are in the anti‐arrangement with two H‐bonds between the N(3) and NH2 of guanine, and NH2 and N(1) of the purin‐2‐amine base (Fig. 4).  相似文献   

15.
In 2‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐1,2,4‐triazine‐3,5(2H,4H)‐dione (6‐aza‐2′‐deoxy­uridine), C8H11N3O5, (I), the conformation of the glycosylic bond is between anti and high‐anti [χ = −94.0 (3)°], whereas the derivative 2‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐N4‐(2‐methoxy­benzoyl)‐1,2,4‐triazine‐3,5(2H,4H)‐dione (N3‐anisoyl‐6‐aza‐2′‐deoxy­uridine), C16H17N3O7, (II), displays a high‐anti conformation [χ = −86.4 (3)°]. The furanosyl moiety in (I) adopts the S‐type sugar pucker (2T3), with P = 188.1 (2)° and τm = 40.3 (2)°, while the sugar pucker in (II) is N (3T4), with P = 36.1 (3)° and τm = 33.5 (2)°. The crystal structures of (I) and (II) are stabilized by inter­molecular N—H⋯O and O—H⋯O inter­actions.  相似文献   

16.
The structures of the isomeric nucleosides 4‐nitro‐1‐(β‐d ‐ribo­furan­osyl)‐1H‐indazole, C12H13N3O6, (I), and 4‐nitro‐2‐(β‐d ‐ribo­furan­osyl)‐2H‐indazole, C12H13N3O6, (II), have been determined. For compound (I), the conformation of the gly­cosylic bond is anti [χ = −93.6 (6)°] and the sugar puckering is C2′‐exo–C3′‐endo. Compound (II) shows two conformations in the crystalline state which differ mainly in the sugar pucker; type 1 adopts the C2′‐endo–C3′‐exo sugar puckering associated with a syn base orientation [χ = 43.7 (6)°] and type 2 shows C2′‐exo–C3′‐endo sugar puckering accompanied by a somewhat different syn base orientation [χ = 13.8 (6)°].  相似文献   

17.
The title compound, C14H16N4O4, adopts the anti conformation at the gly­cosylic bond [χ−117.1 (5)°]. The sugar pucker of the 2′‐deoxy­ribo­furan­osyl moiety is C2′‐endo–C3′‐exo, 2T3 (S‐type). The orientation of the exocyclic C4′—C5′ bond is +sc (gauche). The propynyl group is linear and coplanar with the nucleobase moiety. The structure of the compound is stabilized by several hydrogen bonds (N—H⋯O and O—H⋯O), leading to the formation of a multi‐layered network. The nucleobases, as well as the propynyl groups, are stacked. This stacking might cause the extraordinary stability of DNA duplexes containing this compound.  相似文献   

18.
The title compound {systematic name: 4‐amino‐5‐cyclopropyl‐7‐(2‐deoxy‐β‐D‐erythro‐pentofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine}, C14H18N4O3, exhibits an anti glycosylic bond conformation, with the torsion angle χ = −108.7 (2)°. The furanose group shows a twisted C1′‐exo sugar pucker (S‐type), with P = 120.0 (2)° and τm = 40.4 (1)°. The orientation of the exocyclic C4′—C5′ bond is ‐ap (trans), with the torsion angle γ = −167.1 (2)°. The cyclopropyl substituent points away from the nucleobase (anti orientation). Within the three‐dimensional extended crystal structure, the individual molecules are stacked and arranged into layers, which are highly ordered and stabilized by hydrogen bonding. The O atom of the exocyclic 5′‐hydroxy group of the sugar residue acts as an acceptor, forming a bifurcated hydrogen bond to the amino groups of two different neighbouring molecules. By this means, four neighbouring molecules form a rhomboidal arrangement of two bifurcated hydrogen bonds involving two amino groups and two O5′ atoms of the sugar residues.  相似文献   

19.
Poly(lactic acid) (PLA) stereocomplexes have high potential as renewable materials for advanced polymer applications, mainly due to their high melting temperature (Tm, typically 230–240°C). The properties of PLA stereocomplexes consisting of linear high molar mass homopolymers have been studied extensively in the past, but the available information about the possibilities to affect the thermal properties of the stereocomplex by varying the structure of the blend components has not been sufficient. Novel stereocomplexes containing linear or star‐shaped D ‐lactic acid (D ‐LA) oligomers and high molar mass poly(L ‐lactide) (L‐ PLA) were thus prepared. The Tm and melting enthalpy (ΔHm) of the racemic crystallites were found to depend strongly on both the blending ratio and the arm‐length of the D ‐lactic acid oligomer. The preparation method of the oligomers, i.e. step‐growth polymerization or ring‐opening polymerization (ROP), did not affect the Tm or ΔHm of the blends significantly. Slightly higher ΔHm values were, however, obtained, when linear oligomers were used. The results thus indicated that the Tm and ΔHm of PLA stereocomplexes could be optimized, simply by selecting a D ‐LA oligomer having a suitable arm‐length and structure as the other blend component. The possibility to adjust the melting behavior of the stereocomplex blend is a significant advantage and could make PLA suitable for a wider range of products used at elevated temperatures. Copyright © 2010 John Wiley & Sons, Ltd.  相似文献   

20.
In the title compound [systematic name: 4‐amino‐7‐(β‐d ‐ribofuranos­yl)‐7H‐pyrazolo[3,4‐d][1,2,3]triazine], C9H12N6O4, the torsion angle of the N‐glycosylic bond is high anti [χ = −83.2 (3)°]. The ribofuran­ose moiety adopts the C2′‐endo–C1′‐exo (2T1) sugar conformation (S‐type sugar pucker), with P = 152.4° and τm = 35.0°. The conformation at the C4′—C5′ bond is +sc (gauche,gauche), with the torsion angle γ = 52.0 (3)°. The compound forms a three‐dimensional network that is stabilized by several hydrogen bonds (N—H⋯O, O—H⋯N and O—H⋯O).  相似文献   

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