Recognition of the nonpolar base 4-methylindole in DNA by the DNA repair adenine glycosylase MutY

[formula: see text] The DNA repair adenine glycosylase MutY efficiently recognizes 7-deaza-2'-deoxyadenosine (Z) and its nonpolar isostere 4-methylindole beta-deoxynucleoside (M) opposite 7,8-dihydro-8-oxo-2'-deoxyguanosine (OG) and G in DNA. Both wild-type and truncated MutY exhibit a 10- to 20-fold higher affinity for a duplex containing OG:M than OG:Z. More efficient recognition of M over Z by MutY may be to due the lack of hydrogen bonding with the OG that facilitates nucleotide flipping during the substrate recognition process.     

Probing the requirements for recognition and catalysis in Fpg and MutY with nonpolar adenine isosteres

The Escherichia coli DNA repair enzymes Fpg and MutY are involved in the prevention of mutations resulting from 7,8-dihydro-8-oxo-2'-deoxyguanosine (OG) in DNA. The nonpolar isosteres of 2'-deoxyadenosine, 4-methylbenzimidazole beta-deoxynucleoside (B), and 9-methyl-1H-imidazo[4,5-b]pyridine beta-deoxynucleoside (Q), were used to examine the importance of hydrogen bonding within the context of DNA repair. Specifically, the rate of base removal under single-turnover conditions by the MutY and Fpg glycosylases from duplexes containing OG:B and OG:Q mismatches, relative to OG:A mismatches, was evalulated. The reaction of Fpg revealed a 5- and 10-fold increase in rate of removal of OG from duplexes containing OG:B and OG:Q base pairs, respectively, relative to an OG:A mispair. These results suggest that the lack of the ability to hydrogen bond to the opposite base facilitates removal of OG. In contrast, adenine removal catalyzed by MutY was much more efficient from an OG:A mispair-containing duplex (k2 = 12 +/- 2 min(-1)) compared to the removal of B from an OG:B duplex (k(obs) < 0.002 min(-1)). Surprisingly, MutY was able to catalyze base removal from the OG:Q-containing substrate (k2 = 1.2 +/- 0.2 min(-1)). Importantly, the B and Q analogues are not deleterious to high-affinity DNA binding by MutY. In addition, the B and Q analogues are more susceptible to acid-catalyzed depurination illustrating that the enzyme-catalyzed mechanism is distinct from the nonenzymatic mechanism. Taken together, these results point to the importance of both N7 and N3 in the mechanism of adenine excision catalyzed by MutY.     

Catalytic contributions of key residues in the adenine glycosylase MutY revealed by pH-dependent kinetics and cellular repair assays

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Highlights? Asp 138 must be deprotonated to stabilize the transition state for maximal activity ? Consequences of altering catalytic amino acids in MutY on cellular mismatch repair ? Correlation of MutY enzymatic parameters with ability to mediate cellular repair ? Importance of high affinity binding of MutY to the OG:A mismatch for high levels of repair     

Insights into the role of Val45 and Gln182 of Escherichia coli MutY in DNA substrate binding and specificity

Background  

Escherichia coli MutY (EcMutY) reduces mutagenesis by removing adenines paired with guanines or 7,8-dihydro-8-oxo-guanines (8-oxoG). V45 and Q182 of EcMutY are considered to be the key determinants of adenine specificity. Both residues are spatially close to each other in the active site and are conserved in MutY family proteins but not in Methanobacterium thermoautotrophicum Mig.MthI T/G mismatch DNA glycosylase (A50 and L187 at the corresponding respective positions).     

Transition-state analysis of the DNA repair enzyme MutY

The transition state (TS) structure of MutY-catalyzed DNA hydrolysis was solved using multiple kinetic isotope effect (KIE) measurements. MutY is a base excision repair enzyme which cleaves adenine from 8-oxo-G:A mismatches in vivo, and also from G:A mismatches in vitro. TS analysis of G:A-DNA hydrolysis revealed a stepwise S(N)1 (D(N)*A(N)(double dagger)) mechanism proceeding through a highly reactive oxacarbenium ion intermediate which would have a lifetime in solution of <10(-10) s. C-N bond cleavage is reversible; the N-glycoside bond breaks and reforms repeatedly before irreversible water attack on the oxacarbenium ion. KIEs demonstrated that MutY uses general acid catalysis by protonating N7. It enforces a 3'-exo sugar ring conformation and other sugar ring distortions to stabilize the oxacarbenium ion. Combining the experimental TS structure with the previously reported crystal structure of an abortive Michaelis complex elucidates the step-by-step catalytic sequence.     

Dynamic behavior of DNA base pairs containing 8-oxoguanine

The process by which DNA repair enzymes recognize and selectively excise damaged bases in duplex DNA is fundamental to our mechanistic understanding of these critical biological reactions. 8-Oxoguanine (8-oxoG) is the most common form of oxidative DNA damage; unrepaired, this lesion generates a G:C-->T:A mutation. Central to the recognition and repair of DNA damage is base extrusion, a process in which the damaged base lesion or, in some cases, its partner disengages from the helix and is bound to the enzyme's active site where base excision takes place. The conformation adopted by 8-oxoG in duplex DNA is affected by the base positioned opposite this lesion; conformational changes may also take place when the damaged base binds to its cognate repair enzyme. We performed unrestrained molecular dynamics simulations for several 13-mer DNA duplexes. Oligomers containing G:C and 8oxoG:C pairs adopted Watson-Crick geometries in stable B-form duplexes; 8oxoG showed increased local and global flexibility and a reduced barrier to base extrusion. Duplexes containing the G:A mismatch showed much larger structural fluctuations and failed to adopt a well-defined structure. For the 8oxoG:A mismatch that is recognized by the DNA glycosylase MutY, the damaged nucleoside underwent spontaneous and reproducible anti-->syn transitions. The syn conformation is thermodynamically preferred. Steric hindrance and unfavorable electrostatics associated with the 8oxoG O8 atom in the anti conformation were the major driving forces for this transition. Transition events follow two qualitatively different pathways. The overall anti-->syn transition rate and relative probability of the two transition paths were dependent on local sequence context. These simulations indicate that both the dynamic and equilibrium behavior of the duplex change as a result of oxidation; these differences may provide valuable new insight into the selective action of enzymes on damaged DNA.     

The influence of oxoG on the electronic properties of ds-DNA. Damage versus mismatch: A theoretical approach

The seed of life is concealed in the base sequence in DNA. This macromolecule is continuously exposed to harmful factors which can cause it damage. The stability of genetic information depends on the protein efficiency of repair systems. Glycosylases are the scouts which recognize and remove damaged bases. Their efficiency depends on how rapidly they recognize DNA lesions. One theory states that charge transfer is involved in protein cross talking through ds-DNA. For these reasons a comparative analysis of ds-oligo containing a mismatched base pair dA:::dG and a damaged dA::dG^OXO is proposed. Additionally, the electronic properties of the short ds-oligo in the context of non-equilibrated and equilibrated solvent modes were taken into theoretical consideration. All energetic calculations were performed at the M062x/6-31++G** level of theory, while for geometry optimized ONIOM methodology was used. The lowest adiabatic ionization potential was assigned for DNA containing a dA:dG^OXO pair. Moreover, the adiabatic electron affinity was assigned at the same level for the mismatched and lesioned ds-oligo. Surprisingly, in the non-equilibrated mode, a significantly higher vertical electro affinity was found for lesioned DNA. The higher VEA in a non-equilibrated solvent state supported faster recognition in the A:G^OXO base pair than A:G by MutY glycosylases under electron transfer mechanism.     

Differential Polymorphic Transformation Behavior of Polybutene-1 with Multiple Isotactic Sequences

For the solid-solid transformation from form Ⅱ to form Ⅰ of isotactic polybutene-1(iPB),the temperature dependence of form Ⅰ nucleation and growth was deemed to control the transformation process.However,the relationship between formⅠ formation and form Ⅱ disappearance in the transformation process is not clear.In this work,the spontaneous crystal transformation from form Ⅱ to Ⅰ of iPB with 81 mol%mmmm sequence concentration is studied firstly by tracking the two processes,the decay of form Ⅱ and the yielding of form Ⅰ in a wide range of temperature spanning from 0℃ to 50℃ and in a long transformation time ranging from 5 min to 65 days with in situ FTIR and WAXD.Unlike the literature reports,the decay rate of form Ⅱ is firstly found to be lower than the yielding rate of form Ⅰ at all studied temperatures,especially at low transition temperature.This is attributed to the amorphous chains which locate near crystal lamella participating into the nucleation of form Ⅱ.The regular chain folding and growth of i PB form Ⅰ from amorphous chains containing short isotactic sequences also lead to an increase in crystallinity of form Ⅰ compared with that of initial form Ⅱ crystallized at 60℃.An increase in the annealing temperature results in decrease in crystallinity and increase in lamellae thickness of i PB formⅠ.     

间规聚苯乙烯同质多晶现象的研究

间规聚苯乙烯(ｓＰＳ)是由日本出光公司在1985年首先合成,由于其优良的耐热性(熔点高达270℃),立刻被认为有可能或为下一世纪最重要的工程塑料.独特的分子结构,使间规聚苯乙烯具有密度低、尺寸稳定、耐热性、耐溶剂性好等诸多优点,因而引起研究人员的广泛重视.同时,间规聚苯乙烯存在复杂的同质多晶现象,共有α、β、γ和δ四种晶型.以不同的条件从熔体结晶,间规聚苯乙烯可形成平面锯齿结构的α晶和β晶.其中,α晶属六方晶系,晶胞参数为:ａ=263ｎｍ,ｃ=078ｎｍ;β晶是斜方晶,晶胞参数为:ａ=088ｎｍ,ｂ=263ｎｍ,ｃ=078ｎｍ.与传统的全同聚丙烯…     

Thermally-Induced Phase Transitions in the Uniaxially-Oriented δ Form of Syndiotactic Polystyrene

The empty δ (δ_e) form of uniaxially-oriented syndiotactic polystyrene (sPS) samples were obtained by extracting the solvent molecules from the δ form of sPS and solvent complex in acetone and methanol. Temperature dependence of the X-ray fiber diagrams starting from the uniaxially-oriented δ_e and δ form has been measured successfully at various temperatures for the first time. The transition behavior was traced clearly by separating the equatorial and layer line reflections. The δ_e form transformed to the γ form via an intermediate form. The intermediate form is speculated to take disordered structure due to the empty cavities present in the δ_e form. Calorimetric studies showed an endotherm followed by an exotherm during this phase transition, which is consistant with such a speculation. On the other hand the δ form transformed to the γ form directly without passing through the intermediate form or δ_e form. During the δ to γ phase transition the solvent molecules evaporate through the columnar structure in a broad range of temperature, allowing the transition to occur smoothly.     

Effect of Pre-Existed Form I' on the Phase Transition of Isotactic Poly-1-butene Form III under High Pressure CO2

The CO₂ plasticization effect on the isotactic poly-1-butene (iPB-1) form III with pre-existed minority form I' was investigated by using high-pressure differential scanning calorimetry (DSC). The results showed that the form III melting peak moved to a lower temperature and the melting peak area of form II generated during heating decreased with the increased CO₂ pressure. The solid-solid transition of form III to I' in the iPB-1 was mainly studied by fourier transform infrared spectroscopy (FTIR). It was claimed that the phase transition was a thermodynamic process and the pre-existed form I' in form III inhibit the phase transition of form III into I'. The influence of the pre-existed form I' on the melting behavior of the iPB-1 was also studied by DSC. It was found that the form I' also suppressed the recrystallization of form II.     

Quantification of pharmaceutical polymorphs and prediction of dissolution rate using theophylline tablet by terahertz spectroscopy

Theophylline has an anhydrous form and a monohydrated form, and the dissolution rate of the anhydrous form is higher than that of the monohydrated form. Terahertz (THz) spectra of theophylline tablet containing the theophylline anhydrous form, monohydrated form, microcrystalline cellulose and magnesium stearate exhibited a specific absorption peak at 0.96 THz, where the theophylline anhydrous form demonstrated an absorption peak. Additionally, the intensity of the peak at 0.96 THz gradually decreased as the proportion of the anhydrous form decreased. The multivariate data analysis was performed to correlate the THz spectra of theophylline tablets with the ratio of the theophylline anhydrous form. The calibration model used to predict the mixing ratio of the theophylline anhydrous form from the THz spectra achieved root-mean-squared errors of cross-validation (RMSECV) of 2.89%, a slope of 0.9934 and an R(2) of 0.9927. In addition, there were intentions to develop a prediction model for the dissolution rate of theophylline from the drug product. The dissolution rate of theophylline tablet was gradually delayed as the proportion of the anhydrous form was decreased. The multivariate data analysis was performed to correlate the THz spectra of theophylline tablets with the dissolution rate. The calibration model used to predict the percentage of theophylline dissolved in 45 min from the THz spectra achieved an RMSECV of 3.29%, a slope of 0.9260 and an R(2) of 0.9423. Furthermore, there were no significant differences between the predicted and measured percentages of theophylline dissolved in 45 min in the theophylline tablets that were stored at 84% relative humidity (RH) and 25 °C for 12 h or 3 d.     

Characterization of physical state of mannitol after freeze-drying: effect of acetylsalicylic acid as a second crystalline cosolute

Freeze-drying of mixed solutes is a preparative technique widely used in the pharmaceutical industry. The presence of an amorphous form or changes in the crystalline form can affect solid state stability. In this work, acetylsalicylic acid (AAS) was chosen as a model drug, and was mixed with mannitol, a commonly used bulking agent in formulation of tablets. Variations in the final freeze-dried crystalline forms were found after changing the ratios of the two co-solutes. Samples were analysed by powder X-ray diffractometry and differential scanning calorimetry. A major amorphous form and a minor crystalline delta-mannitol form were produced during the mannitol freeze-drying process. The crystal form of mannitol in the two-component system depended on the AAS:mannitol ratio. The AAS was mostly crystalline, regardless of the amount of mannitol present. A major delta-mannitol and a minor amorphous form were obtained when AAS was present in a high percentage (75% w/w). When AAS percentages of 50 and 25% (w/w) were present during the drying process, the mannitol was found in a highly crystalline form.     

Antifreeze Protein‐Induced Selective Crystallization of a New Thermodynamically and Kinetically Less Preferred Molecular Crystal

The formation of a new, dihydrate crystalline form of 5‐methyluridine (m⁵U) was selectively induced by a protein additive, antifreeze protein (AFP) in a highly efficient manner (in 10^?6 molar scale, whereas known kinetic additives need 0.1 molar scale). The hemihydrate form (form I, the only previously known crystalline form of m⁵U) and the dihydrate form of m⁵U (form II) obtained herein were characterized using X‐ray crystallography and differential scanning calorimetry (DSC). Compared to form I, remarkably, form II is thermodynamically and kinetically less preferred. The presence of AFP can selectively inhibit the appearance of form I and hence allows the growth of form II, the pure form of which cannot grow directly from m⁵U supersaturated solutions under the same conditions. An explanation supported by both experimental and theoretical results is provided for the AFP‐induced selection process. Implications on AFP‐induced ice shape changes are also discussed. Control of crystallization from supersaturated solutions is of great interest in both fundamental research and practical applications in fields like chemistry, pharmacology and materials science. These findings suggest that crystallization processes with AFPs could be valuable for selective growth of hydrates and polymorphs of important pharmaceutical compounds.     

Synthesis, isolation, and characterization of ABT-578 equilibrium isomers

ABT-578, an anti-restenosis agent exists as two isomers, a major pyran form and a minor oxepane form. The existence of the two isomeric forms was established by isolation and equilibration studies under buffered and physiological conditions. Finally their structures were confirmed by converting the major pyran form to the oxepane form by synthesis, isolation, and characterization.     

Ab initio Study of the Keto-Enol Equilibriumof Malonaldehyde

 The mechanism of the keto-enol tautomerism of malonaldehyde was studied by ab initio methods using 6-21G^** and 6-311G^** basis functions at the HF level. Two separate mechanisms were examined: through-space proton transfer in the ω-shaped form and through-space proton transfer in a sickle-shaped form obtained from the ω form by rotation. The transition state structure of the ω form is non-planar, whereas that of the sickle form is planar. The sickle form is connected with a 2^nd order saddle, indicating that there should exist a lower energy barrier, i.e. that the through-bond mechanism may be preferred. The calculated energy barriers of keto-enol tautomerism for the sickle form is twice as high as those for the omega form.     

Polymorphic transformations of Bi2MoO6

The polymorphism of Bi₂MoO₆ has been studied by differential thermal analysis, differential dilatometry, and differential scanning calorimetry with γ form specimens having the koechlinite structure prepared by sintering the oxides Bi₂O₃ and MoO₃. Two stable γ and γ′ forms and one metastable γ″ form were observed. The relative thermal stability of the γ form compared with the γ′ form has been examined by isothermal heating of a mixture of the two forms under hydrothermal conditions. Thus the low-temperature stable γ form transformed reversibly to the γ″ form at 604 ± 3°C, and on subsequent heating, the γ″ form transformed irreversibly to the high-temperature stable γ′ form in the range 640 to 670°C, depending on heating rates; however, an isothermal treatment at a temperature above 604 ± 3°C brought the gradual transition of the γ″ form into the γ′ form.     

Polymorphic Behavior of Syndiotactic Polypropylene Induced by Heat Treatment

The polymorphic behavior of syndiotactic polypropylene (s-PP) crystallized from the melt under different conditions was investigated by means of WAXD and DSC. The isothermal melt crystallization of s-PP proceeded in form I at tc≥ 110℃ and in form Ⅱ at tc≤110 ℃ s-PP crystallized nonisothermally from the melt was the mixture of forms and . With increasing the cooling rate (a), the content of form increased, and the content of form decreased. On heating, at 10 K/min, of quenched s-PP, it crystallized in form at t≤70 , continuing heating resulted in form form transition, which was an endothermal process.     

从硬球微扰理论推导马丁-侯状态方程

从Ｂａｒｈｅｒ－Ｈｅｎｄｅｒｓｏｎ的硬球微扰理论出发，运用幂级数形式的径向分布函数和分段的势能函数导出马丁－侯状态方程，推导过程中导出了一种理论式，计算Ｐ－Ｖ－Ｔ性质的精确度与马丁－侯原式相当，理论式的常数与分子微观参数有确定的函数关系。     

Ab initio Study of the Keto-Enol Equilibriumof Malonaldehyde

Summary.  The mechanism of the keto-enol tautomerism of malonaldehyde was studied by ab initio methods using 6-21G^** and 6-311G^** basis functions at the HF level. Two separate mechanisms were examined: through-space proton transfer in the ω-shaped form and through-space proton transfer in a sickle-shaped form obtained from the ω form by rotation. The transition state structure of the ω form is non-planar, whereas that of the sickle form is planar. The sickle form is connected with a 2^nd order saddle, indicating that there should exist a lower energy barrier, i.e. that the through-bond mechanism may be preferred. The calculated energy barriers of keto-enol tautomerism for the sickle form is twice as high as those for the omega form. Received January 18, 1999. Accepted (revised) August 4, 1999