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1.
Structural modification at the 2′‐O‐position of riboses in oligonucleotide therapeutics is of critical importance for their use as drugs. To date, the methoxyethyl (MOE) substituent is the most important and features in dozens of antisense oligonucleotides that have been tested in clinical trials. Yet, the search for new improved modifications continues in a quest for increased oligonucleotide potency, improved transport in vivo and favorable metabolism. Recently, we described how the conjugation of spermine groups to pyrimidines in oligonucleotides vastly increases their affinity for complementary RNAs through accelerated binding kinetics. Here we describe how spermines can be linked to the exocyclic amino groups of cytidines in MOE‐oligonucleotides employing a straightforward ‘convertible nucleoside approach’ during solid phase synthesis. Singly‐ or doubly‐modified oligonucleotides show greatly enhanced affinity for complementary RNA, with potential for a new generation of MOE‐based oligonucleotide drugs.  相似文献   

2.
Oligodeoxyribonucleotides modified with 5‐[3‐(1‐pyrenecarboxamido)propynyl]‐2′‐deoxyuridine monomer X and proximal LNA monomers display higher affinity for complementary DNA, more pronounced increases in fluorescence emission upon DNA binding, and improved discrimination of SNPs at non‐stringent conditions, relative to the corresponding LNA‐free probes across a range of sequence contexts. The results reported herein suggest that the introduction of LNA monomers influences the position of nearby fluorophores via indirect conformational restriction, a characteristic that can be utilized to develop optimized fluorophore‐labeled probes for SNP‐discrimination studies.  相似文献   

3.
The synthesis of four novel 3′‐C‐branched and 4′‐C‐branched nucleosides and their transformation into the corresponding 3′‐O‐phosphoramidite building blocks for automated oligonucleotide synthesis is reported. The 4′‐C‐branched key intermediate 11 was synthesized by a convergent strategy and converted to its 2′‐O‐methyl and 2′‐deoxy‐2′‐fluoro derivatives, leading to the preparation of novel oligonucleotide analogues containing 4′‐C‐(aminomethyl)‐2′‐O‐methyl monomer X and 4′‐C‐(aminomethyl)‐2′‐deoxy‐2′‐fluoro monomer Y (Schemes 2 and 3). In general, increased binding affinity towards complementary single‐stranded DNA and RNA was obtained with these analogues compared to the unmodified references (Table 1). The presence of monomer X or monomer Y in a 2′‐O‐methyl‐RNA oligonucleotide had a negative effect on the binding affinity of the 2′‐O‐methyl‐RNA oligonucleotide towards DNA and RNA. Starting from the 3′‐C‐allyl derivative 28 , 3′‐C‐(3‐aminopropyl)‐protected nucleosides and 3′‐O‐phosphoramidite derivatives were synthesized, leading to novel oligonucleotide analogues containing 3′‐C‐(3‐aminopropyl)thymidine monomer Z or the corresponding 3′‐C‐(3‐aminopropyl)‐2′‐O,5‐dimethyluridine monomer W (Schemes 4 and 5). Incorporation of the 2′‐deoxy monomer Z induced no significant changes in the binding affinity towards DNA but decreased binding affinity towards RNA, while the 2′‐O‐methyl monomer Z induced decreased binding affinity towards DNA as well as RNA complements (Table 2).  相似文献   

4.
Combining the structural elements of the second generation 2'-O-methoxyethyl (MOE) and locked nucleic acid (LNA) antisense oligonucleotide (AON) modifications yielded the highly nuclease resistant 2',4'-constrained MOE and ethyl bicyclic nucleic acids (cMOE and cEt BNA, respectively). Crystal structures of DNAs with cMOE or cEt BNA residues reveal their conformational preferences. Comparisons with MOE and LNA structures allow insights into their favourable properties for AON applications.  相似文献   

5.
We report the monomer reactivity ratios for copolymers of methyl methacrylate (MMA) and a reactive monomer, 2‐vinyl‐4,4′‐dimethylazlactone (VDMA), using the Fineman–Ross, inverted Fineman–Ross, Kelen–Tudos, extended Kelen–Tudos, and Tidwell–Mortimer methods at low and high polymer conversions. Copolymers were obtained by radical polymerization initiated by 2,2′‐azobisisobutyronitrile in methyl ethyl ketone solutions and were analyzed by NMR, gas chromatography (GC), and gel permeation chromatography. 1H NMR analysis was used to determine the molar fractions of MMA and VDMA in the copolymers at both low and high conversions. GC analysis determined the molar fractions of the monomers at conversions of less than 27% and greater than 65% for the low‐ and high‐conversion copolymers, respectively. The reactivity ratios indicated a tendency toward random copolymerization, with a higher rate of consumption of VDMA at high conversions. For both low‐ and high‐conversion copolymers, the molecular weights increased with increasing molar fractions of VDMA, and this was consistent with the faster consumption of VDMA (compared with that of MMA). © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 3027–3037, 2003  相似文献   

6.
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   

7.
On cooling from the melt, poly(4,4′‐phthaloimidobenzoylnonamethyleneoxycarbonyl) (PEIM‐9) forms a monotropic, smectic liquid crystal phase (Ti = 369.2 K). The main driving force for this mesophase formation is the attainment of nanophase separation of the mobile nonamethylene spacer from the geometrically rigid, but irregular, phthaloimidobenzoyl group, coupled with partial conformational ordering of the CH2 groups (about 20% of the CH2 groups attain trans‐conformations). It is shown by nuclear magnetic resonance that PEIM‐9 consists at room temperature of two motionally distinguishable components. One is the liquid crystal that remains mobile to its glass transition temperature (Tg ≈ 323 K), the other a more rigid crystal with a large degree of conformational disorder. In this crystal phase (Tm ≈ 415 K) the conformationally disordered nonamethylene spacer has a similar amount of disorder than in the liquid crystal phase and the phthaloimidobenzoyl group is also not fully ordered. Even after long‐term annealing, all molecules remain conformationally disordered, but Tm increases to about ≈ 437 K.  相似文献   

8.
3,4′-Substituted aromatic monomers, consisting of two phenylene units joined together by linking groups such as ketone or methylene, have recently been used for the preparation of quasi-rigid fully aromatic thermotropic polymers, based on conformational isomerism, with accessible transition temperatures. In this work the polyester of 3,4′-dicarboxydiphenyl ether and hydroquinone is considered: an Ullmann condensation has been carried out for the preparation of the asymmetric monomer, and low-temperature solution polycondensation has been used to synthesize the polymer. Although a liquid crystalline behavior could be expected, the polyester melts to an isotropic phase. Several copolymers have been prepared, by partially substituting either the asymmetric monomer with terephthalic acid or hydroquinone with different diphenols. The attempt to decrease the stability of the crystalline phase did not lead to significant results. The appearance of the nematic phase in some samples has been attributed to an increased chain stiffness, expressed in terms of persistence length as derived from molecular dynamics (MD) simulations.  相似文献   

9.
The easy‐to‐make 7,7′‐diamino‐2,2′‐diindolylmethane was used as a building block for the construction of anion receptors operating by hydrogen bonds. Its various bisamide and bisurea derivatives were designed and synthesised as acyclic as well as macrocyclic molecules, then their structural and anion binding properties were studied in solution and in the solid state. The bisamide receptors demonstrate high affinity towards oxoanions in highly polar and partially aqueous solutions (DMSO with up to 25 % H2O) with significant selectivity for dihydrogen phosphate. Remarkably, the bisurea‐based molecules are able to bind anionic guests even in pure methanol and show selectivity toward tetrahedral oxoanions, that is, hydrogen sulphate and dihydrogen phosphate. X‐ray analysis revealed that both classes of molecules adopt a similar conformation in the solid state: a bent sheet shape with a binding pocket equipped with hydrogen‐bond donors (four for the amides and six for the bisureas), whose orientation is particularly tailored for oxoanions. The results of ROESY NMR experiments are in agreement with the findings for the solid state and confirmed that both bisamides and bisureas can easily adapt the conformation with convergent hydrogen‐bond donors, which is highly suitable for anion binding.  相似文献   

10.
A simple and straightforward synthesis of 5,5′‐diamino‐4,4′‐dinitramino‐3,3′‐bi‐1,2,4‐triazole by the selective nitration of 4,4′,5,5′‐tetraamino‐3,3′‐bi‐1,2,4‐triazole is presented. The interaction of the amino and nitramino groups improves the energetic properties of this functionalized bitriazole. For a deeper investigation of these properties, various nitrogen‐rich derivatives were synthesized. The new compounds were investigated and characterized by spectroscopy (1H and 13C NMR, IR, Raman), elemental analysis, mass spectrometry, differential thermal analysis (DTA), X‐ray analysis, and impact and friction sensitivities (IS, FS). X‐ray analyses were performed and deliver insight into structural characteristics with which the stability of the compounds can be explained. The standard enthalpies of formation were calculated for all compounds at the CBS‐4M level of theory, revealing highly positive heats of formation. The energetic performance of the new molecules was predicted with the EXPLO5 V6.02 computer. A small‐scale shock reactivity test (SSRT) and a toxicity test gave a first impression of the performance and toxicity of selective compounds.  相似文献   

11.
We demonstrate that conformational‐biased monomers can alter neighboring monomer conformation leading to globe changes in polymer topology. This work is compared to the “sergeants and soldiers” effect observed when a small percentage of optically active monomers control a polymer's helical handedness. Specifically, we show that one biased monomer in a sequence of flexible monomers yields an oligonucleotide block copolymer that folds into two topologies with competitive free energies and activation barriers (from an unfolded state). Double substitutions, on the other hand, have varying degrees of influence depending on the position of the second substitution. Substitutions within the same guanosine block have a lesser effect relative to substitutions in different blocks. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 3271–3278, 2006  相似文献   

12.
NMR spectroscopy was used to characterize the binding of the chiral compound 1,1′‐binaphthyl‐2,2′‐diyl hydrogen phosphate (BNP) to five molecular micelles with chiral dipeptide headgroups. Molecular micelles have covalent linkages between the surfactant monomers and are used as chiral mobile phase modifiers in electrokinetic chromatography. Nuclear overhauser enhancement spectroscopy (NOESY) analyses of (S)‐BNP:molecular micelle mixtures showed that in each solution the (S)‐BNP interacted predominately with the N‐terminal amino acid of the molecular micelle's dipeptide headgroup. NOESY spectra were also used to generate group binding maps for (S)‐BNP:molecular micelle mixtures. In these maps, percentages are assigned to the (S)‐BNP protons to represent the relative strengths of their interactions with a specified molecular micelle proton. All maps showed that (S)‐BNP inserted into a previously reported chiral groove formed between the molecular micelle's dipeptide headgroup and hydrocarbon chain. In the resulting intermolecular complexes, the (S)‐BNP protons nearest to the analyte phosphate group were found to point toward the N‐terminal Hα proton of the molecular micelle headgroup. Finally, pulsed field gradient NMR diffusion experiments were used to measure association constants for (R) and (S)‐BNP binding to each molecular micelle. These K values were then used to calculate the differences in the enantiomers' free energies of binding, Δ(ΔG). The NMR‐derived Δ(ΔG) values were found to scale linearly with electrokinetic chromatography (EKC) chiral selectivities from the literature. Copyright © 2010 John Wiley & Sons, Ltd.  相似文献   

13.
In this work, monomeric molecules (BODIPY) 4,4‐difluoro‐1,2,3,5,7‐pentamethyl‐6‐ethyl‐4‐bora‐3a,4a‐diaza‐s‐indacene ( 1 ), 4,4‐difluoro‐1,7‐dimethyl‐2,3,6‐terethyl‐8‐(4‐tolyl)‐4‐bora‐3a,4a‐diaza‐s‐indacene ( Ph1 ), dimeric monomers (bisBODIPY) 2 , Ph2 , and their packing systems were taken as calculation models to investigate the relationship between monomeric structures and spectral properties of packing systems. Their spectra and carrier transport properties were systemically investigated by density functional theory and time‐dependent DFT methods. The results reveal that dimeric monomers bisBODIPY 2 and Ph2 show significantly bathochromic shift and exhibit a clear exciton splitting in the absorption spectrum compared with those of 1 and Ph1 . Monomeric and dimeric molecules have different monomer conformations (nearly flat and corniform, respectively) and thus diverse packing styles. The intermolecular aggregation affects the excitation energy and oscillator strength of monomers 1 and Ph1 more than those of the corniform monomers 2 and Ph2 . The unique corniform structure of molecules 2 and Ph2 can greatly reduce self‐quenching effect induced by the formation of excimers. This means that suitable modification of molecular arrangement is an effective way to reduce self‐quenching. From the calculation results for molecules Ph1 and 1 , the aryl group at the 8‐position of BODIPY core can hardly affect the optical properties. According to our calculations, BODIPY 1 is a better hole transporter than electron transporter with the internal reorganization energy for hole (λ+) even lower than that of 4,4′‐bis(phenyl‐mtolylamino)biphenyl (TPD), a well‐known hole‐transporting material. Molecules Ph1 , BisBODIPYs 2 , and Ph2 are promising candidate to be excellent ambipolar materials for electroluminescent devices, owing to their quite small and nearly identical reorganization energies for both carriers. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012  相似文献   

14.
9-Mer DNA sequences containing 2'-N-methyl-2'-N-(pyren-1-ylmethyl)-2'-amino-DNA monomers display significantly increased affinity towards DNA complements whereas the corresponding 2'-amino-DNA monomer has a detrimental effect on duplex stability. These effects are efficiently reversed by incorporation of four LNA nucleotides inducing a B-DNA to A-DNA conformational change.  相似文献   

15.
G‐quadruplex (G4) structures carry vital biological functions, and compounds that selectively target certain G4 structures have both therapeutic potential and value as research tools. Along this line, 2,2′‐diindolylmethanes have been designed and synthesized in this work based on the condensation of 3,6‐ or 3,7‐disubstituted indoles with aldehydes. The developed class of compounds efficiently stabilizes G4 structures without inducing conformational changes in such structures. Furthermore, the 2,2′‐diindolylmethanes target certain G4 structures more efficiently than others and this G4 selectivity can be altered by chemical modifications of the compounds.  相似文献   

16.
A novel aromatic diamine monomer, 3,3′‐diisopropyl‐4,4′‐diaminodiphenyl‐3′′,4′′‐difluorophenylmethane (PAFM), was successfully synthesized by coupling of 2‐isopropylaniline and 3,4‐difluorobenzaldehyde. The aromatic diamine was adopted to synthesize a series of fluorinated polyimides by polycondensation with various dianhydrides: pyromellitic dianhydride (PMDA), 3,3′,4,4′‐biphenyltetracarboxylic dianhydride (BPDA), 4,4′‐oxydiphthalic anhydride (ODPA) and 3,3′,4,4′‐benzophenone tetracarboxylic dianhydride (BTDA) via the conventional one‐step method. These polyimides presented excellent solubility in common organic solvents, such as N,N‐dimethylformamide (DMF), N,N‐dimethyl acetamide (DMAc), dimethyl sulfoxide (DMSO), N‐methyl‐2‐pyrrolidone (NMP), chloroform (CHCl3), tetrahydrofuran (THF) and so on. The glass transition temperatures (Tg) of fluorinated polyimides were in the range of 260–306°C and the temperature at 10% weight loss in the range of 474–502°C. Their films showed the cut‐off wavelengths of 330–361 nm and higher than 80% transparency in a wavelength range of 385–463 nm. Moreover, polymer films exhibited low dielectric properties in the range of 2.76–2.96 at 1 MHz, as well as prominent mechanical properties with tensile strengths of 66.7–97.4 MPa, a tensile modulus of 1.7–2.1 GPa and elongation at break of 7.2%–12.9%. The polymer films also showed outstanding hydrophobicity with the contact angle in the range of 91.2°–97.9°.  相似文献   

17.
The minihairpin 5′‐d(GCGAAGC)‐3′ ( 1 ) was modified either in the loop region, in the base‐paired stem, or at the 5′‐terminus by incorporation of base‐modified nucleosides. The thermal melting was correlated to the structural changes induced by the various donor‐acceptor properties of the nucleosides. Overhanging nonpaired nucleosides at the 5′‐terminus stabilized the hairpin, while a reverse of the dG3?dA5 sheared base pair to dA3?dG5 severely affected the stability. The combination of the minihairpin 5′‐d(GCGAAGC)‐3′ ( 1 ) and the thrombin‐binding aptamer 5′‐d(GGTTGGTGTGGTTGG)‐3′ ( 2 (= 46 )) resulted in the new construct 5′‐d(GGTTGGGCGAAGC GGTTGG)‐3′ ( 43 ) arising by replacement of the 5′‐d(TGT)‐3′ loop of 2 by the minihairpin. The fused oligonucleotide 43 exhibits a two‐phase thermal transition indicating the presence of the two unaltered moieties. According to slight changes of the Tm values of the construct 43 as compared to the separate units 1 and 2 , cooperative distorsions are discussed.  相似文献   

18.
The HPLC enantioseparation of nine atropisomeric 3,3′,5,5′‐tetrasubstituted‐4,4′‐bipyridines was performed in normal and polar organic (PO) phase modes using two immobilized polysaccharide‐based chiral columns, namely, Chiralpak IA and Chiralpak IC. The separation of all racemic analytes, the effect of the chiral selector, and mobile phase (MP) composition on enantioseparation and the enantiomer elution order (EEO) were studied. The beneficial effect of nonstandard solvents, such as tetrahydrofuran (THF), dichloromethane (DCM), and methyl t‐butyl ether on enantioseparation was investigated. All selected 4,4′‐bipyridines were successfully enantioseparated on Chiralpak IA under normal or PO MPs with separation factors from 1.14 to 1.70 and resolutions from 1.3 to 6.5. Two bipyridines were enantioseparated at the multimilligram level on Chiralpak IA. Differently, Chiralpak IC was less versatile toward the considered class of compounds and only five bipyridines out of nine could be efficiently separated. In particular, on these columns, the ternary mixture n‐heptane/THF/DCM (90:5:5) as MP had a positive effect on enantioseparation. An interesting phenomenon of reversal of the EEO depending on the composition of the MP for the 3,3′‐dibromo‐5,5′‐bis‐(E)‐phenylethenyl‐4,4′‐bipyridine along with an exceptional enantioseparation for the 3,3′‐dibromo‐5,5′‐bis‐ferrocenylethynyl‐4,4′‐bipyridine (α = 8.33, Rs = 30.6) were observed on Chiralpak IC.  相似文献   

19.
The synthesis of 4,4′‐(arylmethylene)bis‐(3‐methyl‐1‐phenyl‐1H‐pyrazol‐5‐ol) derivatives catalyzed by ʟ‐proline is a simple, versatile, and efficient method. In vitro antioxidant, anti‐inflammatory, and antimicrobial activities of compounds 4a , 4b , 4c , 4d , 4e , 4f , 4g , 4h , 4i , 4j were studied. Furthermore, to rationalize the observed anti‐inflammatory activity data, molecular docking study has been performed against COX‐2 enzyme which revealed a good binding affinity for these molecules and could provide an insight into the various bonded and non‐bonded interactions guiding their binding affinity.  相似文献   

20.
Fluorine substitutions on the furanose ring of nucleosides are known to strongly influence the conformational properties of oligonucleotides. In order to assess the effect of fluorine on the conformation of 3′‐deoxy‐3′‐fluoro‐5‐methyluridine (RTF), C10H13FN2O5, we studied its stereochemistry in the crystalline state using X‐ray crystallography. The compound crystallizes in the chiral orthorhombic space group P212121 and contains two symmetry‐independent molecules (A and B) in the asymmetric unit. The furanose ring in molecules A and B adopts conformations between envelope (2E, 2′‐endo, P = 162°) and twisted (2T3, 2′‐endo and 3′exo, P = 180°), with pseudorotation phase angles (P) of 164.3 and 170.2°, respectively. The maximum puckering amplitudes, νmax, for molecules A and B are 38.8 and 36.1°, respectively. In contrast, for 5‐methyluridine (RTOH), the value of P is 21.2°, which is between the 3E (3′‐endo, P = 18.0°) and 3T4 (3′‐endo and 4′‐exo, P = 36°) conformations. The value of νmax for RTOH is 41.29°. Molecules A and B of RTF generate respective helical assemblies across the crystallographic 21‐screw axis through classical N—H…O aand O—H…O hydrogen bonds supplemented by C—H…O contacts. Adjacent parallel helices of both molecules are linked to each other via O—H…O and O…π interactions.  相似文献   

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