Crystal structure of a continuous three-dimensional DNA lattice

DNA has proved to be a versatile material for the rational design and assembly of nanometer scale objects. Here we report the crystal structure of a continuous three-dimensional DNA lattice formed by the self-assembly of a DNA 13-mer. The structure consists of stacked layers of parallel helices with adjacent layers linked through parallel-stranded base pairing. The hexagonal lattice geometry contains solvent channels that appear large enough to allow 3'-linked guest molecules into the crystal. We have successfully used these parallel base pairs to design and produce crystals with greatly enlarged solvent channels. This lattice may have applications as a molecular scaffold for structure determination of guest molecules, as a molecular sieve, or in the assembly of molecular electronics. Predictable non-Watson-Crick base pairs, like those described here, may present a new tool in structural DNA nanotechnology.     

Assembly of an antiparallel homo-adenine DNA duplex by small-molecule binding

Molecules that reversibly bind DNA and trigger the formation of non-Watson-Crick secondary structures would be useful in the design of dynamic DNA nanostructures and as potential leads for new therapeutic agents. We demonstrate that coralyne, a small crescent-shaped molecule, promotes the formation of a duplex secondary structure from homo-adenine oligonucleotides. AFM studies reveal that the staggered alignment of homo-adenine oligonucleotides upon coralyne binding produces polymers of micrometers in length, but only 2 nm in height. A DNA duplex was also studied that contained eight A.A mismatches between two flanking 7-bp Watson-Crick helices. CD spectra confirm that the multiple A.A mismatches of this duplex bind coralyne in manner similar to that of homo-adenine oligonucleotides. Furthermore, the melting temperature of this hybrid duplex increases by 13 degrees C upon coralyne binding. These observations illustrate that the helical structure of the homo-adenine-coralyne duplex is compatible with the B-form DNA helix.     

Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding?

The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.     

On the nature of ion-stabilized cytosine pairs in DNA i-motifs: The importance of charge transfer processes

Recent experimental results indicate that the stability of non-Watson-Crick DNA i-motif structures can be influenced by the presence of various metal cations. Whereas Au⁺, Cu⁺, and Ag⁺ are stabilizing agents, alkali metal ions like Na⁺ or Li⁺ are known to destabilize the i-motif. In terms of reduced ion-cytosine complexes, we rationalize the experimental observations with the help of standard and conceptual density functional theory (DFT) calculations. Our results highlight the importance of coordinating electrostatic bonds with partially covalent character for the stability of the ion-cytosine complex. The occurrence of these bonds can be mainly attributed to charge transfer processes between two cytosines and the transition metal ions, which can be either explained by frontier molecular orbital theory in combination with a bond critical point analysis, or by the concept of chemical reactivity indices within a conceptual DFT approach. The results of our calculations establish a consistent theoretical framework to understand the experimentally observed behavior, and are also important in order to achieve more detailed insights into nucleobase pairing mechanisms in general.     

Sequence specific fluorescence detection of double strand DNA

Methods for the fluorescent detection of specific sequences of double strand DNA in homogeneous solution may be useful in the field of human genetics. A series of hairpin polyamides with tetramethyl rhodamine (TMR) attached to an internal pyrrole ring were synthesized, and the fluorescence properties of the polyamide-fluorophore conjugates in the presence and absence of duplex DNA were examined. We observe weak TMR fluorescence in the absence of DNA. Addition of >/=1:1 match DNA affords a significant fluorescence increase over equimolar mismatch DNA for each polyamide-TMR conjugate. Polyamide-fluorophore conjugates offer a new class of sensors for the detection of specific DNA sequences without the need for denaturation. The polyamide-dye fluorescence-based method can be used to screen in parallel the interactions between aromatic ring pairs and the minor groove of DNA even when the binding site contains a non-Watson-Crick DNA base pair. A ranking of the specificity of three polyamide ring pairs-Py/Py, Im/Py, and Im/Im-was established for all 16 possible base pairs of A, T, G, and C in the minor groove. We find that Im/Im is an energetically favorable ring pair for minor groove recognition of the T.G base pair.     

Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: the cis- and trans-watson-crick/sugar edge base pair family

The structure and function of RNA molecules are substantially affected by non-Watson-Crick base pairs actively utilizing the 2'-hydroxyl group of ribose. Here we correlate scalar coupling constants across the noncovalent contacts calculated for the cis- and trans-WC/SE (Watson-Crick/sugar edge) RNA base pairs with the geometry of base to base and sugar to base hydrogen bond(s). 23 RNA base pairs from the 32 investigated were found in RNA crystal structures, and the calculated scalar couplings are therefore experimentally relevant with regard to the binding patterns occurring in this class of RNA base pairs. The intermolecular scalar couplings 1hJ(N,H), 2hJ(N,N), 2hJ(C,H), and 3hJ(C,N) were calculated for the N-H...N and N-H...O=C base to base contacts and various noncovalent links between the sugar hydroxyl and RNA base. Also, the intramolecular 1J(N,H) and 2J(C,H) couplings were calculated for the amino or imino group of RNA base and the ribose 2'-hydroxyl group involved in the noncovalent interactions. The calculated scalar couplings have implications for validation of local geometry, show specificity for the amino and imino groups of RNA base involved in the linkage, and can be used for discrimination between the cis- and trans-WC/SE base pairs. The RNA base pairs within an isosteric subclass of the WC/SE binding patterns can be further sorted according to the scalar couplings calculated across different local noncovalent contacts. The effect of explicit water inserted in the RNA base pairs on the magnitude of the scalar couplings was calculated, and the data for discrimination between the water-inserted and direct RNA base pairs are presented. The calculated NMR data are significant for structural interpretation of the scalar couplings in the noncanonical RNA base pairs.     

Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies

The importance of non-Watson-Crick base pairs in the three-dimensional structure of RNA is now well established. The structure and stability of these noncanonical base pairs are, however, poorly understood. We have attempted to understand structural features of 33 frequently occurring base pairs using density functional theory. These are of three types, namely (i) those stabilized by two or more polar hydrogen bonds between the bases, (ii) those having one polar and another C-H...O/N type interactions, and (iii) those having one H-bond between the bases and another involving one of the sugars linked to the bases. We found that the base pairs having two polar H-bonds are very stable as compared to those having one C-H...O/N interaction. Our quantitatively analysis of structures of these optimized base pairs indicates that they possess a different amount of nonplanarity with large propeller or buckle values as also observed in the crystal structures. We further found that geometry optimization does not modify the hydrogen-bonding pattern, as values of shear and open angle of the base pairs remain conserved. The structures of initial crystal geometry and final optimized geometry of some base pairs having only one polar H-bond and a C-H...O/N interaction, however, are significantly different, indicating the weak nature of the nonpolar interaction. The base pair flexibility, as measured from normal-mode analysis, in terms of the intrinsic standard deviations of the base pair structural parameters are in conformity with those calculated from RNA crystal structures. We also noticed that deformation of a base pair along the stretch direction is impossible for all of the base pairs, and movements of the base pairs along shear and open are also quite restricted. The base pair opening mode through alteration of propeller or buckle is considerably less restricted for most of the base pairs.     

Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view

Complex molecular shapes of ribosomal RNA molecules are stabilized by recurrent types of tertiary interactions involving highly specific and conserved non-Watson-Crick base pairs, triplets, and quartets. We analyzed the intrinsic structure and stability of the P-motif and the four basic types of A-minor interactions (types I, II, III, and 0), which represent the most prominent RNA tertiary interaction patterns refined in the course of evolution. In the studied interactions, the electron correlation component of the stabilization usually exceeds the Hartree-Fock (HF) term, leading to a strikingly different balance of forces as compared to standard base pairing stabilized primarily by the HF term. In other words, the A-minor and P-interactions are considerably more influenced by the dispersion energy as compared to canonical base pairs, which makes them particularly suitable to zip the folded RNA structures that are substantially hydrated even in their interior. Continuum solvent COSMO calculations confirm that the stability of the canonical GC base pair is affected (reduced) by the continuum solvent screening considerably more than the stability of the A-minor interaction. Among the studied systems, the strong A-minor II and weak A-minor III interactions require water molecules to stabilize the experimental geometry. Gas-phase optimization of the canonical A-minor II A/CG triplet without water results in a geometry that is clearly inconsistent with the RNA structure. The gas-phase structure of the P-interaction and the most stable A-minor I interaction nicely agrees with the geometries occurring in the ribosome. A-minor I can also adopt an alternative water-mediated substate rather often observed in X-ray and molecular dynamics studies. The A-minor I water bridge, however, does not appear to stabilize the tertiary contact, and its role is to provide structural flexibility to this binding pattern within the context of the RNA structure. Interestingly, the insertion of a polar water molecule in the A-minor I A/CG tertiary contact occurring in the A/C tertiary pair is stabilized primarily by the HF (electrostatic) interaction energy, while the dispersion-controlled A/G contact remains firmly bound. Thus, the intrinsic balance of forces as revealed by quantum mechanics (QM) calculations nicely correlates with many behavioral aspects of the studied interactions inside RNA. The comparison of interaction energies computed using quantum chemistry and an AMBER force field reveals that common molecular mechanics calculations perform rather well, except that the strength of the P-interaction is modestly overestimated. We also briefly discuss the non-negligible methodological differences when evaluating simple base-base nucleic acids base pairs and the complex RNA tertiary base pairing patterns using QM procedures.     

N-异丙基丙烯酰胺/丙烯酸十八酯共聚物水溶液胶束及相分离行为研究

合成了N异丙基丙烯酰胺(NIPAM)和丙烯酸十八酯(ODA)的共聚物.利用荧光探针和滴重法研究了NIPAMODA共聚物在水溶液中的胶束形成过程.同时还利用荧光探针法研究了共聚物水溶液在温度升高时出现的LCST(LowerCriticalSolutionTemperature)现象,表明该高分子在温度升高时存在着相分离现象.利用LB技术测量共聚物不溶单分子膜的PA曲线,发现随着温度升高共聚物的单分子膜越来越凝聚的反常现象,这从另一个侧面证实了共聚物NIPAMODA的相分离行为,并对此现象作了讨论.     

离聚体水基微乳液化的研究——聚苯乙烯离聚体微乳化过程相反转的表征

以乙酰磺酸为磺化剂制备磺化度为３～１５ｍｏｌ％的磺化聚苯乙烯（ＳＰＳ）并中和成盐．在一定的温度和搅拌速率下，加水将ＳＰＳ乳化成水包油的稳定水基微乳液．用乳化过程中体系电导率和粘度的变化表征了乳化相反转过程．研究了溶剂的极性和离子含量对聚苯乙烯离聚体溶液可乳化性和乳化过程及乳液稳定性的影响．     

2.45GHz下常用有机试剂复介电常数的测量与研究

1986年加拿大的R．Gedye和R．J．Giguere等发现了微波可以显著加快有机合成,他们发现用微波辐射可使反应速率和产率有不同程度的提高。由于微波作用机理的特殊性,微波化学对很多化学领域带来了冲击。但是,微波与化学反应体系之间相互作用的一些重大问题还未得到解决,如微波加热过程中化学反应系统的非线性反射、非均匀加热等。解决这类问题,首先必须了解化学反应过程中混合物的电学性质与磁学性质,而物质的宏观电学和磁学性质都用其介电常数和磁导率来描述。对于大部分是非磁性材料的有机试剂,微波与反应体系相互作用的特性集中体现在体系的等效复介电常数上。了解各种常用试剂的复介电常数,可以进一步了解各种化学试剂对微波的吸收和反射的情况。而很多试剂的复介电常数无法从现有文献中得到。本文利用谐振腔微扰法测定了在2．45GHz室温下各类常用有机试剂的复介电常数,结果显示：醇类试剂复介电常数实部与虚部都较大;酮类试剂复介电常数实部相对较大,而虚部较小;酸类试剂复介电常数实部和虚部都较小;烷烃和苯类试剂实部,虚部更小。同时,随着碳链增加,所有试剂的复介电常数的实部与虚部均有下降趋势。这些测试和分析结果将为微波辅助有机合成提供了有益参考。     

乳状液膜体系分离提取铜离子

以Span80-对氨基苯磺酸(APS)-NH3液膜体系分离提取Cu2+。最佳分离条件为:制乳搅拌速度3500r/min,制乳时间及乳水混合时间分别为10min和20min,乳水比和油内比分别为0.38和0.44,APS、Span80和液体石蜡浓度分别为11%、4.4%和2.2%,内相NH3和外相HCl浓度分别为4.0mol/L和0.5mol/L。用该体系分离提取了模拟样中的Cu2+。     

渣油在加氢处理中的性质和结构变化规律研究

利用渣油加氢处理中试装置,获得了经过脱金属催化剂、脱硫催化剂和脱氮催化剂的系列渣油加氢处理产物,分析了各产物的性质。随加氢深度增加,硫、氮、残炭、镍和钒在渣油加氢产物中的的质量分数降低,总脱除率分别为84.9%、51.3%、62.8%、84.8%和94.0%。各产物的组分分布发生变化,饱和分组分增加,芳香分、胶质、沥青质组分减少,重组分胶质和沥青质组分的转化分别达到了57.5%和73.3%。以核磁共振为基础计算了渣油加氢产物组分的平均结构参数。结果表明,芳香分和胶质组分单元结构芳香环数和环烷环数减少,芳香碳分率fA、环烷碳分率fN和烷基碳分率fP变化不明显;而沥青质分子fA增加,fN和fP降低。从平均结构参数还可以看出,不同加氢产物同一种组分在结构上有其共性,但不同组分有明显区别。     

NAD(P)H辅酶模型物结构与反应性关系的研究──3-位酰基的电子效应

合成了一系列3酰胺基氮取代的NAD(P)H模型物,测定了其与5硝基异喹啉正离子的二级反应速率常数,并与模型物的氧化还原电势进行了比较.实验结果表明,模型物3位酰基氧一方面可离域二氢吡啶环上N的电子;另一方面负电性的3位酰基氧在反应过渡态中又可引起分子内和分子间的两种静电作用;3位酰基的电子效应对模型物动力学反应性的影响是这两种效应综合作用的结果.     

5-(2-羧基苯基)-10,15,20-三苯基卟啉对氨基酸酯的分子识别模型研究

对氨基酸及其衍生物的分子识别一直是仿生化学领域中的重要课题.以金属卟啉配合物作为主体分子对氨基酸酯的分子识别是最近几年来的热点之一^[15].氨基酸是蛋白质的主要组成部分,在蛋白质合成过程中,对氨基酸及其衍生物的识别是关健的一步.     

Oxidation of L-lysine by diperiodatocuprate (III) in aqueous alkaline medium by the stopped flow technique

The kinetics of oxidation of L-lysine by diperiodatocuprate (III) (DPC) in alkaline medium at a constant ionic strength of 0.15 mol/dm³ was studied spectrophotometrically. The reaction between DPC and L-lysine in an alkaline medium had a 1: 2 stoichiometry (L-lysine: DPC). The reaction was first order in [DPC] and less than first order in [L-lysine] and [alkali]. The addition of periodate had no effect on the rate of the reaction. The intervention of free radicals was observed in the reaction. The oxidation reaction in alkaline medium was shown to proceed via a DPC-L-lysine complex. The main products were identified by spot test and spectral studies. The reaction constants involved in different steps of the mechanism were calculated. The activation parameters with respect to the slow step of the mechanism were computed and discussed, and thermodynamic values were also determined. The article is published in the original.     

Fe-Al络合催化苯乙烯-马来酸酐交替共聚

应用Ｆｅ（ａｃａｃ）３ Ａｌ（ｉ Ｂｕ）３（ａｃａｃ＝乙酰丙酮）催化苯乙烯 马来酸酐共聚,制得富于交替的白色粉末共聚物．共聚反应动力学研究表明,共聚反应与单体浓度呈一级关系,表观活化能为４８６ｋＪ／ｍｏｌ．     

微波辅助合成分子印迹聚合物用于萃取蜂蜜中的氯霉素

采用微波辅助法快速制备以氯霉素为模板分子的分子印迹聚合物.将合成的聚合物作为吸附剂,选择性分离和富集蜂蜜样品中的氯霉素,并结合高效液相色谱-串联质谱法对萃取物进行分析.对合成的分子印迹聚合物进行了表征,考察了聚合物的吸附性能及其选择性,并进行了Scatchard分析.结果表明,合成的聚合物为球形,对氯霉素具有良好的识别能力,最大表观结合量可达0.428 mmol/g.该方法的线性范围为0.5~100 ng/g,相关系数0.999,蜂蜜中氯霉素的检出限为0.13 ng/g,6种蜂蜜样品中氯霉素的加标回收率范围为88%~93%.     

稀土离子(Ⅲ)与牛血清白蛋白结合作用的研究

模拟生理条件研究了稀土离子(Ⅲ)与牛血清白蛋白(BSA)的结合性质.荧光光谱结果表明,Tb与BSA形成1∶2配合物,表观络合常数lgK=7.93,并由pH电位法得出相近结果.用平衡透析法确定Pr与BSA结合的高亲合位点数为2,低亲合位点数大于6,两类条件结合常数lgK1=5.157,lgK2=3.435.由NMR法通过²³Na弛豫时间的改变可知稀土与BSA络合后蛋白质体积膨胀,活动性增加,相关时间τ_c减小.