Properties of Oligonucleotides with Six Membered Carbohydrate Mimics and a 1,4-Relationship Between the Base Moiety and the Hydroxymethyl Group

Abstract

The properties of oligonucleotides with a six-membered carbohydrate mimic in the backbone structure and a 1,4-relationship between the base moiety and the hydroxymethyl group are summarized. The different six-membered rings that were studied are: 1,5-anhydro-2,3-dideoxy-D-arabino-hexitol, 1,5-anhydro-2-deoxy-D-mannitol, 1,5-anhydro-2-deoxy-D-altritol and 3-hydroxy-4-hydroxymethyl-cyclohexane.     

Aliphatic Amino Acid Side Chains Associate with the “Face” of the Adenine Ring

Abstract

We have synthesized the free amino acid adenylate anydrides of phenylalanine, leucine, isoleucine and valine. These activated compounds are very labile at high pH, but at low pH they become more stable. Proton NMR spectra of these adenylates show that, in every case, the hydrophobic side chains, even in these small molecules at low pH and low concentration, are associated with the “face” of the adenine ring. Although aromatic rings are known to associate with adenine in this fashion, to our knowledge this is the first report of an intercalative-type interaction of aliphatic side chains with nucleic acid bases. Since adenine is the most hydrophobic base, these interactions are of a hydrophobic character, and occur in spite of the fact that the adenine ring is protonated. These results may have implications regarding recognition processes in DNA-protein and RNA-protein interactions.     

Base Dependence of B-DNA Sugar Conformation in Solution and in the Solid State

Abstract

Analysis of 1H-NOESY solution data for eight short DNA duplexes has revealed pronounced differences between the sugar conformations of purine and pyrimidine nucleotides. It was found that the H1′-H4′ interproton distance is less than ca. 3.0 A. in pyrimidine sugars, while in purine sugars it is more than ca. 3.OA. This difference has been analyzed by comparison with the sugar conformations of highly resolved B-DNA crystal structures and model sugar conformations. The conclusion can be drawn that the deoxyribose conformation is of the general C2′-endo type but pyrimidine sugars are characterized by smaller phase angles of pseudorotation P (90°<P<150°), while purine sugars have larger P values that are greater than ca. 140° (140°<P<180°). There is no such clear base dependence of sugar conformation in highly resolved B-DNA crystal structures; however the similar trend can be seen as in the solution studies. Based on B-type DNA crystal structures, I-coupling constants have been calculated, and the applicability of experimental coupling measurements to the determination of sugar conformation is discussed.     

Adenine and Guanine Salvage in Suspension Cultured Cells of Catharanthus roseus

Changes in the activity of adenine and guanine salvage in nucleotideand nucleic acid synthesis during the growth of Catharanthusroseus were investigated. Incorporation of [8-¹⁴C]adenine intoATP and ADP and that of [8-¹⁴C]guanine into GTP and GDP increasedmarkedly in the lag phase of cell growth and then sharply decreased.The incorporation into RNA from both precursors showed a similarpattern. The role of rapid purine salvage observed in the lagphase of cell growth is discussed. Catharanthus roseus, Madagascar periwinkle, suspension culture cells, purine salvage, adenine, guanine     

A Conformational Analysis of the (+) Anti BPDE Adduct to the Guanine Amino Group of dCpdG

Abstract

The (+) anti isomer of benz[a]pyrene diol epoxide (BPDE), 7β, 8a-dihydroxy-9α,10α-epoxy- 7,8,9,10-tetrahydrobenz[a]pyrene has been identified as the probable tumorigenic lesion in mammalian systems. It forms a predominant adduct with DNA at N² of guanine. In order to elucidate its conformation in atomic resolution detail, minimized conformational potential energy calculations were performed for the adduct with dCpdG. A global conformation search involving about 1000 trials was made. The lowest energy conformation had stacking between the hydrocarbon and the adjacent cytidine, in agreement with CD studies on modified GpU and UpG. This conformer differed from the B form most notably in the guanine glycosidic torsion, which is high anti. The next lowest energy form had torsion angles like the B form, with guanine-cytidine stacking. These two conformers differ in energy by only 2.1 kcal./mole, suggesting that their relative stability could easily be reversed in larger polymers, or under specific environmental conditions. Other conformations, with base-hydrocarbon or base-base stacking are also found, at somewhat higher energies. The Z form is at 7.8 kcal./mole. Thus, this adduct stabilizes the B form, in contrast with the N²linked AAF adduct, which stabilizes the Z conformation.     

Interaction Between Analogue Resistance and Amino Acid Auxotrophy in Neurospora

A new p-fluorophenylalanine resistant mutant of Neurospora (fpr-1) was isolated. It is unaffected by the suppressor of a previously described resistance mutant, mtr. The fpr-1 locus is on linkage group V, tightly linked to act-2. The expression of resistance to p-fluorophenylalanine by fpr-1 can be suppressed by genes controlling a requirement for lysine or arginine. The suppression seems to involve an increased sensitivity of the lysine and arginine auxotrophs to p-fluorophenylalanine.     

A Conserved Motif in Intracellular Loop 1 Stabilizes the Outward-Facing Conformation of TmrAB

The ATP binding cassette (ABC) family of transporters moves small molecules (lipids, sugars, peptides, drugs, nutrients) across membranes in nearly all organisms. Transport activity requires conformational switching between inward-facing and outward-facing states driven by ATP-dependent dimerization of two nucleotide binding domains (NBDs). The mechanism that connects ATP binding and hydrolysis in the NBDs to conformational changes in a substrate binding site in the transmembrane domains (TMDs) is currently an outstanding question. Here we use sequence coevolution analyses together with biochemical characterization to investigate the role of a highly conserved region in intracellular loop 1 we define as the GRD motif in coordinating domain rearrangements in the heterodimeric peptide exporter from Thermus thermophilus, TmrAB. Mutations in the GRD motif alter ATPase activity as well as transport. Disulfide crosslinking, evolutionary trace, and evolutionary coupling analysis reveal that these effects are likely due to the destabilization of a network in which the GRD motif in TmrA bridges residues of the Q-loop, X-loop, and ABC motif in the NBDs to residues in the TmrAB peptide substrate binding site, thus providing an avenue for conformational coupling. We further find that disruption of this network in TmrA versus TmrB has different functional consequences, hinting at an intrinsic asymmetry in heterodimeric ABC transporters extending beyond that of the NBDs. These results support a mechanism in which the GRD motifs help coordinate a transition to an outward open conformation, and each half of the transporter likely plays a different role in the conformational cycle of TmrAB.     

Quantum Molecular Modeling of the Interaction Between Guanine and Alkylating Agents - 2 - Nitrogen Mustard

Abstract

The alkylation mechanism of guanine by nitrogen mustard (HN2) was studied by using a supermolecular modeling at the ab initio 6–31G level. Our computations show that interaction of guanine with the aziridinium form of HN2 necessitates a transition state for the N7 alkylation route. The pathway of N7-guanine alkylation by nitrogen and sulfur mustards is discussed on the basis of the Molecular Electrostatic Potential and HOMO-LUMO properties of these molecules.     

Quantum Molecular Modeling of the Interaction Between Guanine and Alkylating Agents - 1 - Sulfur Mustard

Abstract

Interaction between Guanine and the episulfonium form of Sulfur mustard (HD) was studied using the ab initio LCAO-MO method at the HF/6–31G level. The alkylation mechanism on guanine-N7 was analyzed by using a supermolecular modeling. Our stereostructural results associated with the molecular electrostatic potentials and HOMO-LUMO properties, show that in vacuum the alkylation of the N7 of guanine by HD in the agressive episulfonium form is a direct process without transition state and of which the pathway is determined.     

Interaction Between the Glutamine Cycle and the Uptake of Large Neutral Amino Acids in Astrocytes

Abstract: When astrocyte cultures are incubated with glutamate and ammonium, the clearance of these substrates followed by the formation and export of glutamine simulates the action of the "glutamine cycle" that is believed to function in the CNS. In the present study this process was found to increase the uptake of large neutral amino acids (LNAAs), namely, histidine, kynurenine, leucine, phenylalanine, and tryptophan, by two-to threefold in mouse cerebral astrocytes. The enhancement of kynurenine uptake was shown to depend on the formation of glutamine and to saturate at low levels of glutamine. LNAAs transiently lowered the glutamine content of astrocytes that were incubated with glutamate and ammonium, but they did not affect net export of glutamine to the solution at normal physiological pH. However, on adjustment of the pH of the solution to 7.8, which causes a large increase in glutamine content without affecting export, kynurenine now significantly increased net glutamine export. These findings relate to proposed mechanisms of cerebral dysfunction in hyperammonemia.     

壳聚糖中胺基对其抑菌性能的影响及与DNA的作用

采用抑菌圈法研究了壳聚糖对大肠杆菌(E.coli)和金黄色葡萄球菌(St.aureus)的抑菌活性。利用壳聚糖的席夫碱反应,对壳聚糖的胺基进行保护后,研究了壳聚糖中胺基对其抑菌性能的影响。同时,运用紫外吸收光谱和电化学的方法,研究了壳聚糖与DNA的相互作用,提出了壳聚糖对E.coli和St.aureus的抑菌机理。研究结果表明,壳聚糖对E.coli和St.aureus具有很好的抑制作用,且抑菌活性与其胺基有关;壳聚糖能与细胞内带负电的核酸结合,使细胞正常DNA复制生理功能受到影响,抑制细菌的繁殖,从而达到抑菌的目的。     

Conformation of the Flavin Adenine Dinucleotide Cofactor FAD in DNA-Photolyase: A Molecular Dynamics Study

In order to gain insight into the light-driven repair of DNA by the enzyme DNA photolyase, the conformation of the photoactive cofactor FAD, a flavin adenine dinucleotide, has been studied by molecular dynamic simulations. In contrast to FAD in the gas phase and in water where the MD procedure yields various "open" I-shaped as well as "closed" U-shaped conformations, the calculations of FAD binding to the enzyme show essentially a single U-shaped conformation of this cofactor which, so far, is unique among FAD-carrying proteins. It is characteristic for this U-shaped conformation that the FAD components occupy opposite sides of the pocket in the surface of the protein which provides the binding site for the defect pyrimidine dimer structure on DNA. In fact, the calculated U-shaped conformation is very close to the one revealed by the X-ray structure analysis of DNA photolyase. Moreover, the simulations yield details on the binding of the photoactive isoalloxazine moiety and the dynamics of the amino acids forming the binding cavity of the enzyme.     

脆性组氨酸三联体与复制蛋白A相互作用关键氨基酸残基的鉴定

目的：研究脆性组氨酸三联体（Fhit）对ATR/CHK1通路的影响,在确定Fhit与复制蛋白A（RPA）存在相互作用的基础上鉴定Fhit与RPA相互作用的关键氨基酸残基,为进一步研究Fhit特异的信号通路奠定基础。方法：构建一系列Fhit缺失突变体基因Fhit1～Fhit11及6种Fhit点突变体基因,将这些基因插入含GST基因的原核表达载体中,在大肠杆菌中表达并纯化GST-Fhit1～GST-Fhit11融合蛋白、突变体GST-FhitSIYEEL、GST-FhitIY、GST-FhitEL、GST-FhitF、GST-FhitA,以及GST-FhitD融合蛋白,用GST沉降技术研究Fhit与RPA相互作用的关键氨基酸残基。结果：Fhit蛋白第112～117（SIYEEL）残基可能是Fhit与RPA相互作用的关键区域,而第114（Y）残基可能是Fhit与RPA相互作用的关键氨基酸残基。结论：确定了Fhit与RPA相互作用的关键氨基酸残基,为阐明Fhit在维持基因组完整性方面的机理提供了线索。     

Correlation of Amino Acid Sequence and Conformation in Tobacco Mosaic Virus

Correlation of the amino acid sequence with the conformation in tobacco mosaic virus protein is considered in this article. After division of the sequence into groups with helical or nonhelical potential, the segments likely to be helical were related to the X-ray diffraction patterns obtained by Franklin, Caspar, Holmes, and Klug. The approximate locations of these segments within the known boundaries of the subunit were predicted from the radial distribution and helical projection of electron density. As a result of these assignments, the number of possible conformations was also reduced for the nonhelical segments. The structure of the subunit was simulated by flexible models of rubber and electrical tubing, as well as by space-filling Corey-Pauling-Koltun models. These models were used to locate the protein segments impinging upon the ribonucleic acid of the virus. The two pairs of carboxyl groups believed to be responsible for the binding of lead were also tentatively identified on these models as aspartic acid residues 64 and 66 (first pair) and glutamic acid residues 131 and 145 (second pair).     

良种茶树芽叶中氨基酸研究

本文报导利用日立－ＥＧ型氨基酸自动分析仪测定的六个茶树良种芽叶中十九种氨基酸组成情况,并以此为依据对良好的品质风格进行了探讨。     

红菜薹6个品种氨基酸含量的分析比较

对红菜薹6个品种的氨基酸种类、含量进行分析测定,结果表明,红菜薹含有17种氨基酸,其中7种为人体必需氨基酸,各品种间各类氨基酸含量差异不显著;相对于茎干而言,红菜薹的薹叶具有更高的营养价值和药用价值;不同的采收温度对各类氨基酸含量的影响不同。     

The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation

DNA polymerases maintain genomic integrity by copying DNA with high fidelity, part of which relies on the polymerase fingers opening-closing transition, a series of conformational changes during the DNA synthesis reaction cycle. Fingers opening and closing has been challenging to study, mainly due to the need to synchronise molecular ensembles. We previously studied fingers opening-closing on single polymerase-DNA complexes using single-molecule FRET; however, our work was limited to pre-chemistry reaction steps. Here, we advance our analysis to extensible substrates, and observe DNA polymerase (Pol) conformational changes across the entire DNA polymerisation reaction in real-time, gaining direct access to an elusive post-chemistry step rate-limiting for DNA synthesis. Our results showed that Pol adopts the fingers-closed conformation during polymerisation, and that the post-chemistry rate-limiting step occurs in the fingers-closed conformation. We found that fingers-opening in the Pol-DNA binary complex in the absence of polymerisation is slow (～5.3 s^?1), and comparable to the rate of fingers-opening after polymerisation (3.4 s^?1); this indicates that the fingers-opening step itself could be largely responsible for the slow post-chemistry step, with the residual rate potentially accounted for by pyrophosphase release. We also observed that DNA chain-termination of the 3′ end of the primer increases substantially the rate of fingers-opening in the Pol-DNA binary complex (5.3 → 29 s^?1), demonstrating that the 3′-OH residue is important for the kinetics of fingers conformational changes. Our observations offer mechanistic insight and tools to offer mechanistic insight for all nucleic acid polymerases.     

Effect of pH on Adenine and Amino Acid Uptake During Sporulation in Saccharomyces cerevisiae

During the early stages of sporulation in Saccharomyces cerevisiae, the pH of the acetate sporulation medium rises to values of 8.0 or higher. Associated with this rise in pH is a reduced cell permeability to certain precursors of ribonucleic acid (RNA), deoxyribonucleic acid or protein. Uptake of adenine, alanine, and leucine was optimal at pH 5.6 to 6.0, but sporulation was inhibited when the sporulation medium was buffered below pH 7.0. Cellular impermeability can be largely overcome by adjusting the acetate sporulation medium to pH 6.0 for optimal uptake of ¹⁴ C-adenine during short pulses without any apparent effect on sporulation. Sporulating cells pulse-labeled 20 min at pH 6.0 incorporated 40 times more ¹⁴C-adenine into RNA than sporulating cells pulse-labeled at pH 8.0. This increased incorporation can be attributed to a 100-fold increase in labeled adenosine triphosphate in cells pulse-labeled at pH 6.0 where maximum uptake occurs.