碱基对在DNA双螺旋链上分离的自由能计算（英文）

DNA是大部分生物包括病毒的基因载体。DNA双螺旋链通过A=T和G≡C两种碱基对编码实现对遗传信息的存储。碱基对中的相互作用对DNA双螺旋链的稳定性起到重要作用,直接关系到基因的复制和转录。当前研究中,我们构建了四组不同结构的DNA双螺旋链,进行了总共4.3μs的分子动力学模拟。通过伞形取样技术计算了DNA双螺旋链中碱基对分离的自由能曲线,并从分子尺度细节和相互作用能对自由能曲线进行解析。在碱基对G≡C的自由能曲线(PMF-PGC)上观察到三个峰,通过监测氢键数目的变化发现分别对应于G≡C三个氢键的断裂;而在A=T的自由能曲线(PMF-PAT)上只出现一个峰,说明A=T的两个氢键在分离过程中几乎同时断裂。PMF-PGC的总能垒比PMF-PAT高,主要是因为G≡C比A=T多一个氢键,更稳定。两条曲线的后段自由能仍然升高,而此时碱基对的氢键已断裂,这是DNA链骨架刚性所导致。我们还研究了碱基对稳定性受相邻碱基对的影响,发现邻近G≡C碱基对会增强A=T的稳定性,C≡G会削弱A=T的稳定性,T=A对A=T的影响较小。     

碱基对在DNA双螺旋链上分离的自由能计算

DNA是大部分生物包括病毒的基因载体。DNA双螺旋链通过A＝T和G≡C两种碱基对编码实现对遗传信息的存储。碱基对中的相互作用对DNA双螺旋链的稳定性起到重要作用,直接关系到基因的复制和转录。当前研究中,我们构建了四组不同结构的DNA双螺旋链,进行了总共4.3 μs的分子动力学模拟。通过伞形取样技术计算了DNA双螺旋链中碱基对分离的自由能曲线,并从分子尺度细节和相互作用能对自由能曲线进行解析。在碱基对G≡C的自由能曲线(PMF-PGC)上观察到三个峰,通过监测氢键数目的变化发现分别对应于G≡C三个氢键的断裂;而在A＝T的自由能曲线(PMF-PAT)上只出现一个峰,说明A＝T的两个氢键在分离过程中几乎同时断裂。PMF-PGC的总能垒比PMF-PAT高,主要是因为G≡C比A＝T多一个氢键,更稳定。两条曲线的后段自由能仍然升高,而此时碱基对的氢键已断裂,这是DNA链骨架刚性所导致。我们还研究了碱基对稳定性受相邻碱基对的影响,发现邻近G≡C碱基对会增强A＝T的稳定性, C≡G会削弱A＝T的稳定性, T＝A对A＝T的影响较小。     

带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.     

基于i-DNA的电化学pH传感器研究

DNA是生物体内的主要遗传物质,由4种核苷酸A、T、G、C组成.由于它所具有的一些独特性质,使得DNA在纳米器件、生物传感器等的研究中得到越来越多的应用.i-DNA是一段包含胞嘧啶核苷酸(C)的单链DNA片段,当C部分质子化时,由于C和C~+之间的氢键作用,会形成一个四聚体结构.目前,已有多篇文献报道了基于i-DNA的纳米器件~([1～3]).     

液晶气相色谱固定液特殊选择性的研究——Ⅰ.保留指数与柱温关系中常数项的求解法

本文对保留指数与柱温的关系I=A+B/(T+C)进行了讨论。提出可先用两种正构烷烃求出C值,再利用I-1/(T+C)线性关系确定A和B。我们以液晶作为固定液验证了这种方法,并在角鲨烷固定液上与文献作了比较。本文所提供的方法简便、精确,对于评价固定液,预测保留指数及色谱定性等方面有实用意义。     

石墨烯修饰铂电极传感器测定水中微量重金属镉和铅

建立了石墨烯修饰铂电极(G/Pt)共沉积铋膜测定水中微量重金属镉和铅的方法.采用微机电系统(MEMS)工艺制作铂电极,并利用CVD法在铂电极上原位生长石墨烯,制备了石墨烯修饰铂电极,与Ag/AgCl参比电极、铂丝对电极构成三电极体系;采用差分脉冲阳极溶出伏安法对水中微量的镉和铅进行测定.在pH=4.5的醋酸-醋酸钠(HAc-NaAc)底液中,Cd2+和pb2+分别在-0.72和-0.48 V灵敏地产生溶出峰,线性范围分别为0.05 ～ 10 mg/L和0.03 ～5 mg/L,检出限均为10 μg/L.本方法操作简单、安全快速、重现性好,适合于废水、地表水、及生活用水中镉和铅的测定.     

用高效液相色谱法对真核细胞脱氧核糖核酸中碱基含量的研究

]本文提出了一个快速定量测定脱氧核糖核酸DNA）水解产物中各碱基含量的高效液相色谱法。在HypersilODS柱上,用06M醋酸钠,4甲醇(pH7)作洗脱液,可将胞嘧啶(C)、尿嘧啶(U)、鸟嘌呤(G)、胸腺嘧啶(T)、腺嘌呤(A);五种碱基基线分离。方法简便,12分钟可完成分离,取样量0.3克或更少,最低检出极限约5毫微克（30pmole,标准偏差在0.1～0.8。对中、幼年小白鼠全脑,小牛胸腺,鱼精DNA中的碱基进行了测定,结果与文献值基本一致。     

硫黄素T与侧翼连接双链DNA的G-四链体高特异性作用

富G碱基的DNA序列在离子诱导下可形成G-四链体(G4),基于这一构型转化设计了大量的传感检测平台。其中的荧光检测平台是基于G4与荧光小分子的相互作用。但是,G4与荧光小分子的有效结合依赖于G4构型和体系中存在的离子种类和离子浓度,尤其是高Na⁺浓度(140 mmol·L^-1)。那么如何实现G4与荧光小分子普适性地有效结合,并不依赖于体系中的Na⁺和Na⁺浓度,是一个难题。在本研究中,以最简单的富G DNA序列凝血酶适体链TBA (thrombin binding aptamer)为例,在3’端和5’端分别增加10个碱基(TBA-10 bp),K⁺诱导TBA-10 bp形成K⁺稳定TBA (K⁺-TBA,G4)并衔接含有10个互补碱基对的双链DNA (K⁺-TBA-10 bp)。相较于K⁺-TBA,硫磺素T与K⁺-TBA-10 bp结合后的荧光强度增加了100倍,相互作用强度增加了1000倍,而且与体系中的Na⁺ (5-140 mmol·L^-1)无关。结合荧光光谱,紫外吸收光谱和圆二色光谱发现硫磺素T特异性的嵌合于K⁺-TBA和双链DNA衔接处的空腔内。有趣的是,这一结合模式不受G4构型的影响。该研究结果为研究G4与荧光小分子的有效结合提供了新视角,也为拓展G4在生物功能和生化检测领域的应用提供了实验依据。     

反相高效液相法测定大鼠肝组织中DNA的碱基含量

 利用反相高效液相法 ,采用SupelcosilLC 18柱 (2 5 0mm× 4 6mmi d ,5 μm) ,以甲醇 0 0 5mol/LKH2 PO4缓冲液 (体积比为 2 0∶80 )为流动相 ,流速 0 8mL/min ,在 2 5 4nm波长处检测 ,对生活在高原 (海拔 2 3km)的习服大鼠肝组织中脱氧核糖核酸 (DNA)的碱基含量进行了检测 ,发现各碱基在DNA中所占的比例是相对稳定的 :腺嘌呤 (A) 2 8 8%、鸟嘌呤 (G) 2 3 3%、胞嘧啶 (C) 17 4 %、胸腺嘧啶 (T) 2 5 3% ,并利用内标法对DNA甲基化水平进行了测定。     

B—DNA分子中互补碱基对G—C、A—T水合作用的研究

本文通过对B—DNA分子中互补碱基对A—T、G—C水合作用的量子化学计算以及最优化处理求得了它们水合作用的最优配位模式。结果表明,当水分子与互补碱基对A—T、G—C共面且水分子与A—T碱基对中胸腺嘧啶(T)杂环上的O_2原子形成氢键以及与G—C碱基对中胞嘧啶(C)杂环上的O_2原子形成氢键时,它们的水合作用具有最稳定的配位模式。     

DNA碱基激光拉曼光谱检测方法的研究

以激光拉曼光谱仪采集腺嘌呤(A)、鸟嘌呤(G)、胞嘧啶(C)、胸腺嘧啶(T)的拉曼光谱图,分析了各碱基谱峰归属,并依据归属结果检测混合碱基组成。结果显示:4种碱基的特征峰集中在175～1 800cm~(-1)。相同积分时间和激光功率条件下,该波段内嘌呤碱基的激光拉曼光谱峰高于嘧啶碱基的谱峰。腺嘌呤、鸟嘌呤、胞嘧啶、胸腺嘧啶分别在723、648、791、1 368 cm~(-1)处的谱峰最强,利用这些特征峰能在2min内鉴别出混合碱基中的各碱基。     

Direct electrochemistry of DNA,guanine and adenine at a nanostructured film-modified electrode

A nanostructured film electrode, a multi-wall carbon nanotubes (MWNT)-modified glassy carbon electrode (GCE), is described for the simultaneous determination of guanine and adenine. The properties of the MWNT-modified GCE were investigated by scanning electron microscopy (SEM) and cyclic voltammetry. The oxidation peak currents of guanine and adenine increased significantly at the MWNT-modified GCE in contrast to those at the bare GCE. The experimental parameters were optimized and a direct electrochemical method for the simultaneous determination of guanine and adenine was proposed. Using the MWNT-modified GCE, a sensitive and direct electrochemical technique for the measurement of native DNA was also developed, and the value of (G+C)/(A+T) of HCl-digested DNA was detected.     

CH3CH2+O(3P)反应机理的理论研究

The reaction for CH3CH2+O(3P) was studied by ab initio method. The geometries of the reactants, intermediates, transition states and products were optimized at MP2/6-311+G(d,p) level. The corresponding vibration frequencies were calculated at the same level. The single-point calculations for all the stationary points were carried out at the QCISD(T)/6-311+G(d,p) level using the MP2/6-311+G(d,p) optimized geometries. The results of the theoretical study indicate that the major products are the CH2O＋CH3, CH3CHO+H and CH2CH2+OH in the reaction. For the products CH2O＋CH3 and CH3CHO+H, the major production channels are A1: (R)→IM1→TS3→(A) and B1: (R)→IM1→TS4→(B), respectively. The majority of the products CH2CH2+OH are formed via the direct abstraction channels C1 and C2: (R)→TS1(TS2)→(C). In addition, the results suggest that the barrier heights to form the CO reaction channels are very high, so the CO is not a major product in the reaction.     

Direct NMR detection of alkali metal ions bound to G-quadruplex DNA

We describe a general multinuclear (1H, 23Na, 87Rb) NMR approach for direct detection of alkali metal ions bound to G-quadruplex DNA. This study is motivated by our recent discovery that alkali metal ions (Na+, K+, Rb+) tightly bound to G-quadruplex DNA are actually "NMR visible" in solution (Wong, A.; Ida, R.; Wu, G. Biochem. Biophys. Res. Commun. 2005, 337, 363). Here solution and solid-state NMR methods are developed for studying ion binding to the classic G-quadruplex structures formed by three DNA oligomers: d(TG4T), d(G4T3G4), and d(G4T4G4). The present study yields the following major findings. (1) Alkali metal ions tightly bound to G-quadruplex DNA can be directly observed by NMR in solution. (2) Competitive ion binding to the G-quadruplex channel site can be directly monitored by simultaneous NMR detection of the two competing ions. (3) Na+ ions are found to locate in the diagonal T4 loop region of the G-quadruplex formed by two strands of d(G4T4G4). This is the first time that direct NMR evidence has been found for alkali metal ion binding to the diagonal T4 loop in solution. We propose that the loop Na+ ion is located above the terminal G-quartet, coordinating to four guanine O6 atoms from the terminal G-quartet and one O2 atom from a loop thymine base and one water molecule. This Na+ ion coordination is supported by quantum chemical calculations on 23Na chemical shifts. Variable-temperature 23Na NMR results have revealed that the channel and loop Na+ ions in d(G4T4G4) exhibit very different ion mobilities. The loop Na+ ions have a residence lifetime of 220 micros at 15 degrees C, whereas the residence lifetime of Na+ ions residing inside the G-quadruplex channel is 2 orders of magnitude longer. (4) We have found direct 23Na NMR evidence that mixed K+ and Na+ ions occupy the d(G4T4G4) G-quadruplex channel when both Na+ and K+ ions are present in solution. (5) The high spectral resolution observed in this study is unprecedented in solution 23Na NMR studies of biological macromolecules. Our results strongly suggest that multinuclear NMR is a viable technique for studying ion binding to G-quadruplex DNA.     

205Tl NMR methods for the characterization of monovalent cation binding to nucleic acids

Monovalent cations play an important role in many biological functions. The guanine rich sequence, d(G4T4G4), requires monovalent cations for formation of the G-quadruplex, d(G4T4G4)2. This requirement can be satisfied by thallium (Tl+), a potassium (K+) surrogate. To verify that the structure of d(G4T4G4)2 in the presence of Tl+ is similar to the K+-form of the G-quadruplex, the solution structure of the Tl+-form of d(G4T4G4)2 was determined. The 10 lowest energy structures have an all atom RMSD of 0.76 +/- 0.16 A. Comparison of this structure to the identical G-quadruplex formed in the presence of K+ validates the isomorphous nature of Tl+ and K+. Using a 1H-205Tl spin-echo difference experiment we show that, in the Tl+-form of d(G4T4G4)2, small scalar couplings (<1 Hz) exist between 205Tl and protons in the G-quadruplex. These data comprise the first 1H-205Tl scalar couplings observed in a biological system and have the potential to provide important constraints for structure determination. These experiments can be applied to any system in which the substituted Tl+ cations are in slow exchange with the bulk ions in solution.     

Impact of pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure

Design of novel DNA probes to inhibit specific repair pathways is important for basic science applications and for use as therapeutic agents. As shown previously, single pyrophosphate (PP) and O-ethyl-substituted pyrophosphate (SPP) modifications can inhibit the DNA glycosylase activities on damaged DNA. To understand the structural basis of this inhibition, the influence of the PP and SPP internucleotide groups on the helical parameters and geometry of a double-stranded DNA was studied by using molecular modeling tools including molecular dynamics and quantum mechanical-molecular mechanical (QM/MM) approaches. Native and locally modified PP- and SPP-containing DNA duplexes of dodecanucleotide d(C1G2C3G4A5A6T7T8C9G10C11G12) were simulated in aqueous solution. The energies and forces were computed by using the PBE0/6-31+G** approach in the QM part and the AMBER force-field parameters in the MM part. Analysis of the local base-pair helical parameters, internucleotide distances, and overall global structure at the located stationary points revealed a close similarity of the initial and modified duplexes, with only torsion angles of the main chain being altered in the vicinity of introduced chemical modification. Results show that the PP and SPP groups are built into a helix structure without elongation of the internucleotide distance due to flipping-out of phosphate group from the sugar-phosphate backbone. The mechanism of such embedding has only a minor impact on the base pairs stacking and Watson-Crick interactions. Biochemical studies revealed that the PP and SPP groups immediately 5', but not 3', to the 8-oxoguanosine (8oxodG) inhibit translesion synthesis by a DNA polymerase in vitro. These results suggest that subtle perturbations of the DNA backbone conformation influence processing of base lesions.     

Carbon-to-carbon identity proton transfer from allene, ketene, ketenimine, and thioketene to their respective conjugate anions in the gas phase. An ab initio study.

Gas-phase acidities of CH2=C=X (X = CH2, NH, O, and S) and barriers for the identity proton transfers (X=C=CH2 + HC triple bond C-X- right harpoon over left harpoon -X-C triple bond CH + CH2=C=X) as well as geometries and charge distributions of CH2=C=X, HC triple bond C-X- and the transition states of the proton transfer were determined by ab initio methods at the MP2/6-311+G(d,p)//MP2/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory. The acidities were also calculated at the CCSD(T)/6-311+G(2df,p) level. A major objective of this study was to examine how the enhanced unsaturation of CH2=C=X compared to that of CH3CH=X may affect acidities, transition state imbalances, and intrinsic barriers of the identity proton transfer. The results show that the acidities are all higher while the barriers are lower than for the corresponding CH3CH=X series. The transition states are all imbalanced but less so than for the reactions of CH3CH=X.     

FAAS法测定ZYSP喷金料中高含量锡

用盐酸(1+1)和硝酸(1+1)混合液溶解ZYSP喷金料,并采用富火焰原子吸收法在锡的次灵敏线286.3nm处对样液中高含量的锡进行直接测试。线性范围0～250mg·L~(-1),其灵敏度为3.10mg·L~(-1)/1％吸收,回收率为100.1％～103.7％,相对标准偏差不大于3.5％,并用标准加入法进行对照。