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1.
Tandemly activated tRNAs, bearing amino acid moieties at both the 2'- and 3'-positions of the 3'-terminal adenosine moiety (A(76)), have been shown to participate efficiently in protein synthesis [B. Wang, J. Zhou, M. Lodder, R. D. Anderson, III and S. M. Hecht, J. Biol. Chem., 2006, 281, 13865]. The mechanism by which such activated tRNAs are able to donate both amino acids to the growing polypeptide chain is not well understood. Here we report the chemical behavior and participation in protein synthesis of new bisaminoacyl derivatives of pdCpA and tRNA. Both amino moieties of the aminoacyl groups are shown to be important to enable participation in protein synthesis; paradoxically, they also confer an unanticipated chemical stability toward different nucleophiles. The results obtained suggest a model for participation of bisaminoacylated tRNAs in protein synthesis.  相似文献   

2.
Nucleoside phosphoramidates (NPs) are a class of nucleotide analogues that has been developed as potential antiviral/antitumor prodrugs. Recently, we have shown that some amino acid nucleoside phosphoramidates (aaNPs) can act as substrates for viral polymerases like HIV‐1 RT. Herein, we report the synthesis and hydrolysis of a series of new aaNPs, containing either natural or modified nucleobases to define the basis for their differential reactivity. Aqueous stability, kinetics, and hydrolysis pathways were studied by NMR spectroscopy at different solution pD values (5–7) and temperatures. It was observed that the kinetics and mechanism (P? N and/or P? O bond cleavage) of the hydrolysis reaction largely depend on the nature of the nucleobase and amino acid moieties. Aspartyl NPs were found to be more reactive than Gly or β‐Ala NPs. For aspartyl NPs, the order of reactivity of the nucleobase was 1‐deazaadenine>7‐deazaadenine>adenine>thymine≥3‐deazaadenine. Notably, neutral aqueous solutions of Asp‐1‐deaza‐dAMP degraded spontaneously even at 4 °C through exclusive P? O bond hydrolysis (a 50‐fold reactivity difference for Asp‐1‐deaza‐dAMP vs. Asp‐3‐deaza‐dAMP at pD 5 and 70 °C). Conformational studies by NMR spectroscopy and molecular modeling suggest the involvement of the protonated N3 atom in adenine and 1‐ and 7‐deazaadenine in the intramolecular catalysis of the hydrolysis reaction through the rare syn conformation.  相似文献   

3.
The self-organization of random copolymers composed of a nucleobase monomer (either 1-(4-vinylbenzyl)thymine or 9-(4-vinylbenzyl)adenine) and dodecyl methacrylate (DMA) was studied in dilute chloroform solutions. The balance between the molar fractions of the nucleobase monomer (leading to intermolecular H-bonding) and DMA (soluble moiety in chloroform) in the polymer chains was found to be the parameter that principally influences the self-organization. DMA-rich copolymers are molecularly soluble in chloroform, whereas nucleobase-rich copolymers are insoluble in this solvent. Copolymers possessing an equimolar comonomer composition self-assemble into micrometer-sized particles physically cross-linked by intermolecular H-bonds (either thymine-thymine or adenine-adenine interactions, depending on the studied copolymer). Nevertheless, when mixed together, thymine- and adenine-based colloids fuse into thermodynamically stable microspheres cross linked by adenine-thymine interactions.  相似文献   

4.
The synthesis, crystal structure and variable-temperature magnetic measurements of the compounds [Mn(mu-ox)(H2O)(7H-pur-kappaN9)]n (1), {[Mn(mu-ox)(H2O)2].(7H-ade).(H2O)}n (2) and {[Cu(mu-ox)(H2O)(7H-ade-kappaN9)][Cu(mu-ox)(mu-H2O)(7H-ade-kappaN9)]. approximately 10/3H2O}n (3), (where ox: oxalato dianion, pur: purine, and ade: adenine) are reported. Compounds 1and 2 contain one-dimensional chains in which manganese(II) atoms are bridged by bis-bidentate oxalato ligands. The distorted octahedral geometry around each metal centre is completed in compound 1 by one water molecule and the imidazole N9 donor site of the purine ligand, which is a rare example of direct binding between the Mn(II) ion and the N donor site of an isolated nucleobase. Unlike 1, the adenine moiety in compound 2 is not bonded to manganese atoms and the metal coordination polyhedron is filled by two water molecules in a cis-arrangement. Its crystal building is constructed from pi-stacked layers of Watson-Crick hydrogen-bonded adenine...(H2O2)...adenine aggregates and zig-zag Mn(II)-oxalato chains held together by means of a strong network of hydrogen bonding interactions. The nucleobase exists in the lattice as the 7H-adenine tautomer which represents an unprecedented solid-state characterization of this minor tautomer as free molecule (without metal coordination) stabilized through non-covalent interactions. Compound consists of two slightly different [Cu(ox)(H2O)(7H-ade-kappaN9)] units in which the nucleobase coordinates through the imidazole N9 atom. The planar complex entities are parallel stacked and joined by means of long Cu-O bonds involving oxygen atoms from the oxalato and the aqua ligands, giving one-dimensional chains with a [4 + 1] square-planar pyramidal and a [4 + 2] octahedral coordination around the metal centre, respectively. Self-assembled process of compound 3 is further driven by an in-plane network of hydrogen bonding interactions to generate a porous 3D structure containing parallel channels filled by guest water molecules. Variable-temperature magnetic susceptibility measurements of all the complexes show the occurrence of antiferromagnetic interactions between the paramagnetic centres. DFT calculations have been performed to check the influence of packing in the stability of the 7H-amino tautomer of 2 and in the complex geometry of 3.  相似文献   

5.
NMR experiments and theoretical investigations were performed on hydrogen bonded complexes of specifically 1- and 7-15N-labeled adenine nucleosides with carboxylic acids. By employing a freonic solvent of CDClF2 and CDF3, NMR spectra were acquired at temperatures as low as 123 K, where the regime of slow hydrogen bond exchange is reached and several higher-order complexes were found to coexist in solution. Unlike acetic acid, chloroacetic acid forms Watson-Crick complexes with the proton largely displaced from oxygen to the nitrogen acceptor in an ion pairing structure. Calculated geometries and chemical shifts of the proton in the hydrogen bridge favorably agree with experimentally determined values if vibrational averaging and solvent effects are taken into account. The results indicate that binding a second acidic ligand at the adenine Hoogsteen site in a ternary complex weakens the hydrogen bond to the Watson-Crick bound carboxylic acid. However, substituting a second adenine nucleobase for a carboxylic acid in the trimolecular complex leads to cooperative binding at Watson-Crick and Hoogsteen faces of adenosine.  相似文献   

6.
The stability constants of the 1:1 complexes formed between Pb2+ and the nucleosides (Ns), adenosine and guanosine, as well as between the nucleotides (NMP2-), AMP2-, IMP2-, and GMP2-, were determined by potentiometric pH titrations in aqueous solution (25 degrees C; I = 0.1 M, NaNO3). Based on previously established log KPb(R-PO3)Pb versus pKH(R-PO3)H straight-line plots (R-PO3(2-) = simple phosphate monoester or phosphonate ligands where R is a noninteracting site), it is shown that the Pb(IMP) and Pb(GMP) complexes are more stable than is expected on the basis of the basicity of the phosphate group of IMP2- and GMP2-. This means that macrochelates are formed, where the phosphate-coordinated Pb2+ also interacts with N7 of the nucleobase residue. In contrast, the stability of the Pb(AMP) complex is governed by the basicity of the AMP2- phosphate group. These results agree with the observations made for the Pb(Ns)2+ complexes: Pb(adenosine)2+ is very unstable in contrast to Pb(guanosine)2+, the stability of which is very similar to the one of Pb(cytidine)2+ studied previously. The stability constants of the Pb(Ns)2+ complexes also allowed an evaluation of the structure in solution of the monoprotonated Pb(H;NMP)+ complexes, the stabilities of which were also determined. We were able to show that the proton is located at the phosphate group and Pb2+ at the N7/(C6)O site of H(GMP)-; in the case of H(AMP)- Pb2+ is probably about equally distributed between the adenine residue and the monoprotonated phosphate group. On the basis of the stability constants of these complexes and their structures in solution, it is possible to provide a series which reflects the decreasing affinity for Pb2+ of nucleobase residues in single-stranded nucleic acids: guanine approximately equal to cytosine > (hypoxanthine) > adenine > uracil approximately equal to thymine. The Pb2+ affinity of the phosphodiester linkage, -PO3(-)-, is similar to the one of the adenine residue, but is expected to be more significant due to its larger abundance. The relevance of these results for lead-activated ribozymes is briefly discussed.  相似文献   

7.
The synthesis of adenophostin A (2) and two analogues [etheno adenophostin (4) and 8-bromo adenophostin (5)] modified at the adenine moiety, is reported. A combination of NMR analysis and molecular modelling was used to compare their structures in solution and determined that they all adopt very similar conformations. The analogues were tested for their ability to mobilise Ca(2+) from DT40 cells expressing recombinant Type 1 rat Ins(1,4,5)P(3)R which reveals etheno adenophostin as a high affinity fluorescent probe of the Ins(1,4,5)P(3)R. 8-Bromo adenophostin was only slightly less potent. The biological results support our current hypothesis regarding the binding mode of adenophostin A at the Ins(1,4,5)P(3)R, i. e. that a cation-pi interaction between the base moiety and Arg 504 of the receptor in combination with H-bonding may be responsible for the high potency of adenophostin A relative to Ins(1,4,5)P(3).  相似文献   

8.
A novel hydrogen bond-forming ligand for pyrimidine/purine transversion, which contains both a fluorescent naphthyridine moiety and a ferrocenyl group as an electrochemical indicator, is described. Hydrogen bond-mediated recognition for a target nucleobase at an abasic site in a DNA duplex is confirmed by both fluorescence and electrochemical measurements. The analysis by fluorescence titration reveals that the ligand shows significant fluorescent quenching upon formation of a 1 : 1 complex with the target nucleobase opposite the abasic site, and the selectivity is in the order of cytosine > thymine > adenine, guanine, reflecting the stability of the hydrogen bond formation.  相似文献   

9.
Synchrotron radiation circular dichroism (SRCD) spectra of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides and cyclic derivatives were measured in the vacuum ultraviolet region (down to 168 nm for sugars and 175 nm for adenine derivatives) and at different pH values (3, 6-7, 9-10) and temperatures (between 5 and 45 degrees C). The information content in the VUV region is important since the CD bands strongly depend on the chemical structure of the sugar, the presence and orientation of a phosphate group and the protonation state of adenine. On the other hand, single or double deprotonation of the phosphoric acid group has no influence on the spectra. We assign the vacuum ultraviolet (VUV) CD bands of the nucleoside and nucleotides to be due mainly to n-->pi* transitions in the adenine nucleobase based on a comparison with the absorption spectra. The CD bands of the sugars are due to n(O -->sigma*) transitions and are much smaller than the CD signal from the nucleotides in the VUV region. Bands are assigned to both pyranose and open-chain forms.  相似文献   

10.
Recently discovered new chemical entities in RNA modifications have involved surprising functional groups that enlarge the chemical space of RNA. Using LC‐MS, we found over 100 signals of RNA constituents that contained a ribose moiety in tRNAs from E. coli. Feeding experiments with variegated stable isotope labeled compounds identified 37 compounds that are new structures of RNA modifications. One structure was elucidated by deuterium exchange and high‐resolution mass spectrometry. The structure of msms2i6A (2‐methylthiomethylenethio‐N6‐isopentenyl‐adenosine) was confirmed by methione‐D3 feeding experiments and by synthesis of the nucleobase. The msms2i6A contains a thioacetal, shown in vitro to be biosynthetically derived from ms2i6A by the radical‐SAM enzyme MiaB. This enzyme performs thiomethylation, forming ms2i6A from i6A in a first turnover. The new thioacetal is formed by a second turnover. Along with the pool of 36 new modifications, this work describes a new layer of RNA modification chemistry.  相似文献   

11.
RNA functionalization is challenging due to the instability of RNA and the limited range of available enzymatic reactions. We developed a strategy based on solid phase synthesis and post‐functionalization to introduce an electrophilic site at the 3′ end of tRNA analogues. The squarate diester used as an electrophile enabled sequential amidation and provided asymmetric squaramides with high selectivity. The squaramate‐RNAs specifically reacted with the lysine of UDP‐MurNAc‐pentapeptide, a peptidoglycan precursor used by the aminoacyl‐transferase FemXWv for synthesis of the bacterial cell wall. The peptidyl‐RNA obtained with squaramate‐RNA and unprotected UDP‐MurNAc‐pentapeptide efficiently inhibited FemXWv. The squaramate unit also promoted specific cross‐linking of RNA to the catalytic Lys of FemXWv but not to related transferases recognizing different aminoacyl‐tRNAs. Thus, squaramate‐RNAs provide specificity for cross‐linking with defined groups in complex biomolecules due to its unique reactivity.  相似文献   

12.
Fluorescent supramolecular nucleoside-based organogels or hydrogels have attracted increasing attention owing to their tunable stability,drug delivery,tissue engineering,and inherent biocompatibility for applications in designing sensors.As the temperature of a constant TPE-Octa-dU gelato r at MGC as low as 0.2 wt% was increased with gel to sol transition,a progressive decrease in the fluorescence intensity was observed.~1 H NMR study in ethanol-d_6/H_2 O revealed the existence of intermolecular hydrogen-bond interaction between uridine nucleobase and triazole moieties.Based on these experiments,thus organogels induced by hydrogen bonding can promote an aggregation-induced emission(AIE) of TPE moiety.Thermoreversible gelation properties have been investigated systematically,including AIE-shapemorphing architecture owing to their unique solid-liquid interface and easy processability.At the same line,the related TPE-EdU derivative which was synthesized from 5-ethynyl-2'-deoxyuridine does not delive r organogels or hydrogels,a nd under similar circumstances TPE moiety of TPE-EdU does not efficiently exhibit AIE phenomenon either.  相似文献   

13.
A new structure for an adenine-selective host molecule, featuring the pertinent link of five-six-five-membered heteroaromatic rings and two carbamoyl NH sites, was developed. This structure provides a correctly oriented array of complementary hydrogen bonding sites for the adenine nucleobase, which exploits both Watson-Crick and Hoogsteen-type interactions. The complexation with adenine nucleobases by multiple hydrogen bonding was supported by (1)H NMR spectroscopy. This type of host displayed high selectivity in complexation, with an accompanying fluorescent response to lipophilized adenosine in CHCl(3). Furthermore, a remarkably selective potentiometric response was attained for adenosine 5'-monophosphate over 5'-GMP, 5'-CMP, and 5'-UMP by using an ion-selective electrode with a PVC-supported solvent polymeric membrane. This indicates recognition of water-soluble nucleotide guests through the membrane-water interface. These findings are expected to form a reliable basis for the development of artificial sensing systems for mononucleotides in biological systems.  相似文献   

14.
《Tetrahedron》2019,75(37):130497
Structurally modified nucleoside analogues are a major source of therapeutic agents and building blocks for incorporation into synthetic oligonucleotides able to interfere with information transfer or other biological functions. This work describes the synthesis of non-natural l-nucleoside phosphonate mimics containing two anomeric centers. Such compounds feature either a di- or monohydroxy tetradialdose sugar as the glycone unit, while adenine is present as nucleobase. By judicious use of protecting groups at the 2- and 3-position of commercial 1-O-acetyl-2,3,5-tri-O-benzoyl-β-d-ribofuranose, both the phosphonate and nucleobase moieties were stereoselectively introduced to provide a dihydroxylated compound with cis-configured substituents as the sole reaction product. Subsequent selective deprotection and deoxygenation at the 3′-position occurred smoothly to afford the corresponding 4′-monohydroxy tetradialdose containing analogue.  相似文献   

15.
We here show that the pKa (error limit: 0.01 to 0.03 pKa unit) of a nucleobase in a nucleotide can be modulated by the chemical nature of the 2'-substituent at the sugar moiety. This has been evidenced by the measurement of nucleobase pKa in 47 different model nucleoside 3',5'-bis- and 3'-mono-ethylphosphates. The fact that the electronic character of each of the 2'-substituents (Fig. 1) alters the chemical shift of the H2' sugar proton, and also alters the pKa of the nucleobase in the nucleotides has been evidenced by a correlation plot of pKa of N3 of pyrimidine (T/C/U) or pKa of N7 of 9-guaninyl with the corresponding deltaH2' chemical shifts at the neutral pH, which shows linear correlation with high Pearson's correlation coefficients (R = 0.85-0.97). That this modulation of the pKa of the nucleobase by a 2'-substituent is a through-bond as well as through-space effect has been proven by ab initio determined pKa estimation. Interestingly, experimental pKas of nucleobases from NMR titration and the calculated pKas (by ab initio calculations utilizing closed shell HF 6-31G** basis set) are linearly correlated with R = 0.98. It has also been observed that the difference of ground and protonated/de-protonated HOMO orbital energies (DeltaHOMO, a.u.) for the nucleobases (A/G/C/T/U) are well correlated with their pK(a)s in different 2'-substituted 3',5'-bis-ethylphosphate analogs suggesting that only the orbital energy of HOMO can be successfully used to predict the modulation of the chemical reactivity of the nucleobase by the 2'-substituent. It has also been demonstrated that pKa values of nucleobases in 3',5'-bis-ethylphosphates (Table 1) are well correlated with the change in dipole moment for the respective nucleobases after protonation or de-protonation. This work thus unambiguously shows that alteration of the thermodynamic stability (Tm) of the donor-acceptor complexes [ref. 20], as found with various 2'-modified duplexes in the antisense, siRNA or in triplexes by many workers in the field, is a result of alteration of the pseudoaromatic character of the nucleobases engineered by alteration of the chemical nature of the 2'-substitution.  相似文献   

16.
L-Dopa, the standard therapeutic for Parkinson's disease, is inactivated by the enzyme catechol-O-methyltransferase (COMT). COMT catalyzes the transfer of an activated methyl group from S-adenosylmethionine (SAM) to its catechol substrates, such as L-dopa, in the presence of magnesium ions. The molecular recognition properties of the SAM-binding site of COMT have been investigated only sparsely. Here, we explore this site by structural alterations of the adenine moiety of bisubstrate inhibitors. The molecular recognition of adenine is of special interest due to the great abundance and importance of this nucleobase in biological systems. Novel bisubstrate inhibitors with adenine replacements were developed by structure-based design and synthesized using a nucleosidation protocol introduced by Vorbrüggen and co-workers. Key interactions of the adenine moiety with COMT were measured with a radiochemical assay. Several bisubstrate inhibitors, most notably the adenine replacements thiopyridine, purine, N-methyladenine, and 6-methylpurine, displayed nanomolar IC(50) values (median inhibitory concentration) for COMT down to 6 nM. A series of six cocrystal structures of the bisubstrate inhibitors in ternary complexes with COMT and Mg(2+) confirm our predicted binding mode of the adenine replacements. The cocrystal structure of an inhibitor bearing no nucleobase can be regarded as an intermediate along the reaction coordinate of bisubstrate inhibitor binding to COMT. Our studies show that solvation varies with the type of adenine replacement, whereas among the adenine derivatives, the nitrogen atom at position 1 is essential for high affinity, while the exocyclic amino group is most efficiently substituted by a methyl group.  相似文献   

17.
用分子动力学模拟的方法揭示了结构水分子在糖原合成酶激酶-3β(GSK-3β)中的作用. 如果没有结构水, ATP嘌呤环的结合位置将发生偏移以填补结构水留下的空间; ATP结合口袋中的氢键网络将被破坏, 保守残基Lys85与ATP的磷酸根侧链只能形成一个保守氢键, 无法维持磷酸根转移所需的线性关系; 由于失去了氢键网络的稳定作用, Glu97和Lys85会向远离ATP的方向移动, 并导致Arg96的侧链发生偏转, 使Arg96无法保持与Arg180和Lys205之间正常的相对位置, 最终影响GSK-3β与底物的结合.  相似文献   

18.
The direct monoacylation of diols by acyl phosphate monoesters in water is a biomimetic analogy to the enzymic aminoacylation of tRNA by aminoacyl adenylates. Without catalysis, acyl phosphate monoesters react rapidly with amines but very slowly with water and alcohols. Lanthanide ions dramatically and selectively facilitate the base-catalyzed monoacylation of diols in water by methyl benzoyl phosphate (MBP), a typical acyl phosphate monoester, in neutral solutions where reactive amines are protonated and unreactive. The reaction patterns and reactivity of various diols with MBP in the presence of lanthanides are consistent with a mechanism that involves internal addition from the conjugate base of the bis-bidentate complex of the lanthanide with the diol and MBP. The method is also applicable to reactions of nucleosides as evidenced by the selective monoacylation of the 2'- or 3'-hydroxyl group of adenosine, without reaction of the 5'-hydroxyl group or the 6-amino group. Analogues of adenosine without the diol are unreactive. This suggests that the method will selectively monoacylate the hydroxyl groups at the unique diol in tRNA that forms the 3'-terminus.  相似文献   

19.
A novel calix[4]arene linked nucleobase molecular receptor bearing two adenine moieties has been synthesized and characterized by UV, IR, NMR and ESI–MS analyses. The synthesized receptor can recognize biologically important Zn2+ and Mn2+ ions through 1:1 binding stoichiometry. The evaluation of binding constants suggests that adenine alone, in an appropriate supramolecular network, can exhibit efficient binding for Zn2+ ions without the presence of any phosphate or sugar unit.  相似文献   

20.
The conjugation of the NCN-pincer platinum(II) complexes as an oraganometallic compound and the uracil derivatives as a nucleobase was demonstrated to give the corresponding bioorganometallics. The NCN-pincer ligands bearing the 6-ethynyl-1-octyluracil, 5-ethynyl-1-octyluracil, and the furanopyrimidine moiety were synthesized. In a crystal state, the NCN-pincer ligand bearing the 6-ethynyl-1-octyluracil moiety was found to form a hydrogen-bonded dimer through intermolecular hydrogen bonds between the uracil moieties, which was connected through π-π interaction between the uracil and benzene moieties of the NCN-pincer ligand. The reaction of the NCN-pincer ligand bearing the 6-ethynyl-1-octyluracil moiety with [Pt(tolyl-4)2(SEt2)]2 led to the formation of the NCN-pincer platinum(II) complex bearing the 6-ethynyl-1-octyluracil moiety. The NCN-pincer platinum(II) complex bearing the furanopyrimidine moiety was obtained by the reaction of the NCN-pincer ligand bearing the furanopyrimidine moiety with [Pt(tolyl-4)2(SEt2)]2. The single-crystal X-ray structure determination of the NCN-pincer platinum(II) complex bearing the furanopyrimidine moiety revealed the formation of the furanopyrimidine ring and the π stack dimer between the furanopyrimidine and benzene moieties of the NCN-pincer ligand in the crystal packing. The NCN-pincer platinum(II) complexes bearing the 6-ethynyl-1-octyluracil moiety or the furanopyrimidine moiety exhibited emission in both solution and solid states.  相似文献   

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