Energetic basis of molecular recognition in a DNA aptamer

The thermal stability and ligand binding properties of the L-argininamide-binding DNA aptamer (5'-GATCGAAACGTAGCGCCTTCGATC3') were studied by spectroscopic and calorimetric methods. Differential calorimetric studies showed that the uncomplexed aptamer melted in a two-state reaction with a melting temperature T-m = 50.2 +/- 0.2 degrees C and a folding enthalpy Delta H degrees(fold) = -49.0 +/- 2.1 kcal mol(-1). These values agree with values of T-m = 49.6 degrees C and Delta H degrees(fold) = -51.2 kcal mol(-1) predicted for a simple hairpin structure. Melting of the uncomplexed aptamer was dependent upon salt concentration, but independent of strand concentration. The T of aptamer melting was found to increase as L-argininamide concentrations increased. Analysis of circular dichroism titration data using a single-site binding model resulted in the determination of a binding free energy Delta G degrees(bind) = -5.1 kcal mol(-1). Isothermal titration calorimetry studies revealed an exothermic binding reaction with Delta H degrees(bind) = -8.7 kcal mol(-1). Combination of enthalpy and free energy produce ail unfavorable entropy of -T Delta S degrees = +3.6 kcal mol(-1). A molar heat capacity change of -116 cal mol(-1) K-1 was determined from calorimetric measurements at four temperatures over the range of 15-40 degrees C. Molecular dynamics simulations were used to explore the structures of the unligated and ligated aptamer structures.

Molecular imprinting of nitrophenol and hydroxybenzoic acid isomers: effect of molecular structure and acidity on imprinting

Three nitrophenol isomer-imprinted polymers were prepared under the same conditions using 4-vinylpyridine as a functional monomer. Different recognition capacities for template molecules were observed for the three polymers. Another imprinting system with stronger acidity than nitrophenol isomers, 2-hydroxybenzoic acid (salicylic acid) and 4-hydroxybenzoic acid, was imprinted using 4-vinylpyridine or acrylamide as functional monomer respectively. Both 4-hydroxybenzoic acid-imprinted polymers using the two monomers showed recognition ability for the template molecule. However, when acrylamide was chosen as functional monomer, the salicylic acid-imprinted polymer showed very weak recognition for the template molecule, whereas strong recognition ability of the resultant polymer for salicylic acid was observed with 4-vinylpyridine as functional monomer. It seems that the structure and acidity of template molecules is responsible for the difference in recognition, by influencing the formation and strength of interaction between template molecule and functional monomer during the imprinting process. An understanding of the mechanism of molecular imprinting and molecular recognition of MIPs will help to predict the selectivity of MIPs on the basis of template molecule properties. Copyright (C) 2003 John Wiley Sons, Ltd.

Adaptive recognition of small molecules by nucleic acid aptamers through a label-free approach

We report a novel label-free method for the investigation of the adaptive recognition of small molecules by nucleic acid aptamers using capillary electrophoresis analysis. Cocaine and argininamide were chosen as model molecules, and the two corresponding DNA aptamers were used. These single-strand DNAs folded into their specific secondary structures, which were mainly responsible for the binding of the target molecules with high affinity and specificity. For molecular recognition, the nucleic acid structures then underwent additional conformational changes, while keeping the target molecules stabilized by intermolecular hydrogen bonds. The intrinsic chemical and physical properties of the target molecules enabled them to act as indicators for adaptive binding. Thus any labeling or modification of the aptamers or target molecules were made obsolete. This label-free method for aptamer-based molecular recognition was also successfully applied to biological fluids and therefore indicates that this approach is a promising tool for bioanalysis.

CE with electrochemical detection for investigation of label-free recognition of amino acid amides by guanine-rich DNA aptamers

In this work, we report a simple and effective investigation into adaptive interactions between guanine-rich DNA aptamers and amino acid amides by CE with electrochemical (EC) detection. Argininamide (Arm) and tyrosinamide (Tym) were chosen as model molecules. On a copper electrode, Arm generated a good EC signal in 60 mM NaOH at 0.7 V (vs Ag/ AgCl), while Tym. was detected well on a platinum electrode at 1. 3 V in 20 mM phosphate of pH 7.0. Based on their EC properties, the ligands themselves were used as indicators for the adaptive interactions investigated by CE-EC, making any step of labeling and/or modification of aptamers with indicators exempted. Hydrophilic ionic liquid was used as an additive in running buffer of CE to improve the sensitivity of Arm detection, whereas the additive was not used for Tym. detection due to its negative effect. Two guanine-rich DNA aptamers were used for molecular recognition of Arm and Tym. When the aptamers were incubated with ligands, they bound the model molecules with high affinity and specificity, reflected by obvious decreases in the signals of ligands but no changes in those of the control molecules. However, the ligands were hardly affected by the control ssDNAs after incubation. The results revealed the specific recognition of Arm and Tym. by the aptamers.

Aptamer-based label-free method for hemin recognition and DNA assay by capillary electrophoresis with chemiluminescence detection

An aptamer-based label-free approach to hemin recognition and DNA assay using capillary electrophoresis with chemiluminescence detection is introduced here. Two guanine-rich DNA aptamers were used as the recognition element and target DNA, respectively. In the presence of potassium ions, the two aptamers folded into the G-quartet structures, binding hemin with high specificity and affinity. Based on the G-quartet-hemin interactions, the ligand molecule was specifically recognized with a K (d)approximate to 73 nM, and the target DNA could be detected at 0.1 mu M. In phosphate buffer of pH 11.0, hemin catalyzed the H2O2-mediated oxidation of luminol to generate strong chemiluminescence signal; thus the target molecule itself served as an indicator for the molecule-aptamer interaction, which made the labeling and/or modification of aptamers or target molecules unnecessary. This label-free method for molecular recognition and DNA detection is therefore simple, easy, and effective.

Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Molecular component structures mediated formation of self-assemblies

Molecular recognition directed self-assemblies from complementary molecular components, melamine and barbituric acid derivatives were studied by means of NMR, fluorescence, and TEM. It was found that both the process of the self-assembly and the morphologies of the resulted self-assemblies could be mediated by modifying the structures of the molecular components used. The effect of the structures of the molecular components on the formation of the self-assemblies was discussed in terms of intermolecular interactions.

Electro-mass olfactory multi-sensor (EMMS)

For an olfactory sensor or electronic nose, the task is not only to detect the object concentration, but also to recognize it. It is well known that all the elements can be identified by their charge to mass ratio e(+)/m. We tried to imitate this principle for molecular recognition. Two kinds of sensors are used simultaneously in testing. One is quartz crystal microbalance (QCM) for detecting the change in mass, the other is interdigital electrode (IE) for detecting the change in conduction, as an electro-mass multi-sensor (EMMS). in this paper, the principle and the feasibility of this method are discussed. The preliminary results on the recognition of alcohol by EMMS coated with lipids are presented. Meanwhile, the multi-sensor can also be used as an instrument for research on some physico-chemistry problems. The change in conduction of coated membrane caused by one absorbed molecule is reported. It is found that when a QCM is coated with membrane, it still obeys the relationship Delta F (frequency change of QCM) = K Delta m (mass change of absorbed substance) and the proportional coefficient, K, depends not only on quartz properties but also on membrane characteristics as well. (C) 2000 Elsevier Science S.A. All rights reserved.

基于核酸特殊结构的分子识别及核酸相关纳米结构的设计应用

核酸为生命的最基本物质之一，是生物体遗传信息的携带者，在生长、遗传、变异等一系列重大生命现象中起决定性的作用。以核酸作为新药设计的靶分子，越来越受到人们的广泛重视。然而，不像其它靶分子如蛋白质、受体等具有特定的结构和功能，核酸结构在很多情况下是同源的，而且联系到很多人体正常的生理功能；能够与核酸结合的药物又往往不具有序列选择性，这就带来明显的毒副作用。因此，寻找和发现一些与疾病相关的核酸的特殊结构，并筛选对其有特异性结合能力的小分子，是以核酸为靶的药物研究的一个重要课题。 近年来，随着纳米科学技术的兴起，以核酸作为纳米体系的结构材料开始受到人们的广泛关注。作为一类特殊的线性高分子，核酸具有化学性质稳定，结构丰富且可控，良好的刚性和柔性，精确识别，高度生物相容性，合成方便等诸多优点，是一类优良的结构材料。目前核酸相关的纳米组装结构和器件研究还处于起步阶段，但是已经呈现出良好的发展前景。 本论文主要针对核酸特殊结构的分子识别及核酸相关功能纳米结构的设计这两方面展开了研究，全文由以下两大部分组成： 第一部分通过光谱学和生物化学等手段，研究了小分子对不同核酸结构的识别作用。借助于竞争平衡透析技术，发现一类恶嗪染料(oxazine dyes)能够与多种结构核酸结合。热变性及光谱实验结果表明，oxazine染料能够诱导杂合体三链核酸poly(rA):2poly(dT)的形成，并强烈地稳定其结构，其中以cresyl violet作用最强，是迄今发现的化合物中最强的。进一步研究发现，此类化合物以嵌插方式与杂合体三链核酸结合。RNase H酶切实验表明，杂合体三链核酸的形成能够强烈地抑制RNase H核酸酶的活性。研究了oxazine-170与三链核酸poly(dA):2poly(dT)及poly(rA):2poly(rU)的相互作用，发现oxazine-170能够强烈稳定三链DNA poly(dA):2poly(dT)的结构，而对相应双链DNA不具稳定作用；对三链RNA poly(rA):2poly(rU)及相应的双链RNA都有一定稳定作用，但作用不强。进一步研究发现，oxazine-170能够以两种结合方式与核酸结合：嵌插方式和外部静电堆积作用。研究了oxazine-170及cresyl violet与单链核酸的相互作用。研究发现oxazine-170能够序列特异性地与单链核酸poly(rA) 结合，CD光谱及AFM研究发现oxazine-170诱导poly(rA)形成新的二级结构。UV光谱、FL光谱及RLS研究发现poly(rA)促使oxazine 170形成H-aggregate，并以poly(rA)为模板自组装。而cresyl violet能够与单链核酸poly(rA)及poly(dA)结合，且采用不同的结合方式： cresyl violet能够与oxazine-170 类似地以poly(rA)为模板自组装；以嵌插方式与poly(dA)结合，并诱导其单链碱基堆积方式的改变。通过以上实验结果，我们进一步揭示了oxazine染料作为肿瘤细胞染色及光动力学治疗试剂的结构基础，对进一步设计、合成更加高效的抗肿瘤药物具有一定的指导意义。 第二部分中，我们尝试设计了几种基于核酸的纳米结构功能体系，并讨论了其相关应用。利用有机小分子coralyne能够诱导聚腺嘌呤序列反平行双链结构的形成，实现了一类新型的小分子诱导的纳米金组装结构。并以(dA)16功能化的金纳米粒子作为新型纳米探针，发展了一种简单的筛选单链核酸聚腺嘌呤序列结合分子的筛选方法。利用核酸限制性内切酶酶切位点回文序列的结构特点，设计了一种以DNA功能化的金纳米粒子组装体为酶切底物的比较通用的核酸限制性内切酶活力检测方法，并进一步用于甲基化酶活性检测及其抑制剂的筛选。基于单链DNA富胞嘧啶i-motif结构在不同pH值条件下的形成与解离，设计了一类质子驱动的DNA分子镊子，与基于链交换反应的DNA分子镊子相比，该体系更加简单，工作效率更高。随后，我们又通过合理设计，得到了两种分别能够结合与释放DNA和蛋白的分子镊子，为其应用做了一些探索。

Electro-mass multi odor sensor

For an olfactory sensor or electronic nose the task is not only to detect the object concentration, but also to recognize it. It is well known that all the elements can be identified by their charge to mass ratio e+/m. We tried to use this principle for molecular recognition. Two kinds of sensors are used simultaneously in testing. One is Quartz Crystal Microbalance (QCM) for detecting the change in mass, the other is Interdigital Electrode (IE) for detecting the change in conduction. In this paper the principle and the feasibility of this method are reported. The preliminary results on the recognition of alcohols are presented. The multisensor can be used as an instrument for research on material properties and kinetic process as well.

Electro-mass olfactory multi-sensor (EMMS)

For an olfactory sensor or electronic nose, the task is not only to detect the object concentration, but also to recognize it. It is well known that all the elements can be identified by their charge to mass ratio e(+)/m. We tried to imitate this principle for molecular recognition. Two kinds of sensors are used simultaneously in testing. One is quartz crystal microbalance (QCM) for detecting the change in mass, the other is interdigital electrode (IE) for detecting the change in conduction, as an electro-mass multi-sensor (EMMS). in this paper, the principle and the feasibility of this method are discussed. The preliminary results on the recognition of alcohol by EMMS coated with lipids are presented. Meanwhile, the multi-sensor can also be used as an instrument for research on some physico-chemistry problems. The change in conduction of coated membrane caused by one absorbed molecule is reported. It is found that when a QCM is coated with membrane, it still obeys the relationship Delta F (frequency change of QCM) = K Delta m (mass change of absorbed substance) and the proportional coefficient, K, depends not only on quartz properties but also on membrane characteristics as well. (C) 2000 Elsevier Science S.A. All rights reserved.

融合蛋白方法制备顺序酶传感器

针对顺序酶传感器酶膜活力低、互换性差的难题，该研究以麦芽糖传感器为研究对象，提出了融合蛋白的解决方案，建立了融合蛋白技术制备顺序酶传感器的模式方法.该研究首次将融合蛋白技术引入生物传感器的研究，成功地构建了具有双酶活力的融合蛋白，建立了融合蛋白技术制备顺序酶传感器的模式方法，为解决顺序酶传感器灵敏度和互换性差的难题提供了新的途径，同时也为解决其它顺序酶反应的低效率问题提供了一种新思路.

环糊精衍生物的设计、合成及其对环辛烯光异构化研究

环糊精(Cyclodextrins, CDs)经化学修饰后可以得到各种类型的衍生物，不仅可以扩展其原有的键合能力，而且还可以改变其选择性，是当代超分子化学的一个研究热点。环糊精第二面的仲羟基比第一面的伯羟基有着更好的催化性能，第二面的选择性修饰将产生更多有价值的衍生物，可用于催化、酶模拟、手性识别等方面。 取代苯甲酰基修饰环糊精对顺式环辛烯(cis-cyclooctene)光异构化反应有非常重要的影响作用，苯环上取代基的性质和取代位置与产物的%ee值和对映体构型之间存在某种内在联系。有目的地选择适宜取代基，设计、合成新型环糊精光增感剂, 有可能按预定目的得到更高%ee值的反式环辛烯；同时，取代苯甲酰基修饰环糊精对cis-cyclooctene光异构化的增感机理有待于进一步阐明。 本论文工作对环糊精的化学修饰以及超分子体系对cis-cyclooctene不对称光异构化反应方面的进展进行了调研。合成了一系列单-6-位取代苯甲酰基修饰环糊精，用于cis-cyclooctene光异构化增感反应，并用圆二色光谱滴定法研究这些环糊精衍生物与cis-cyclooctene的相互作用，以探索光增感反应机理。在此基础上，探讨了环糊精第二面的选择性修饰方法。内容主要包括： 1. 简要介绍了超分子化学的概况，并对环糊精的选择性修饰方法和超分子体系对cis-cyclooctene不对称光异构化反应的主要成果和最新进展进行了评述。 2. 合成了12种单-6-O-(取代苯甲酰基)-β-环糊精，其中10种为新化合物。采用紫外光谱、红外光谱、核磁共振波谱以及质谱等手段对化合物的结构进行了表征。 3. 探索了直接选择性修饰环糊精第二面的便捷新方法。用取代苯甲酰咪唑酯为酰化试剂，0.2M碳酸盐缓冲溶液(pH=9.9)作催化剂，能够有效地活化2-位仲羟基，对环糊精第二面进行选择性修饰，此方法既简便又经济；同时，发现取代苯甲酰基能够在β-CD第二面的2-位、3-位羟基间相互迁移。 4. 用单-6-O-(取代苯甲酰基)-β-环糊精作光增感剂，对cis-cyclooctene光异构化反应进行研究。实验结果证明：取代苯甲酰基上的取代基性质、位置、长度对反应的对映选择性有很大影响；此外，反应体系溶剂极性对产物的%ee值和对映体构型也有重大影响。用单-6-O-(3-甲氧苯甲酰基)-β-CD作增感剂，cis-cyclooctene光异构化反应产物(R)-trans-cyclooctene的对映选择性为45.8%ee，是到目前为止取得的最好对映选择性。 5. 采用圆二色光谱滴定法研究环糊精衍生物与cis-cyclooctene的相互作用，计算包结物的平衡常数，研究包结物的相对稳定性，为探索光增感反应机理提供基础。我们猜测：电子效应对cis-cyclooctene光异构化反应的影响，可能比取代基位置对反应的影响更大，借助电子效应有希望获得更高的%ee值。 Cyclodextrins can be subjected to diverse modifications to give a wide variety of cyclodextrin derivatives, which could not only extend their original molecular binding ability, but also alter their molecular selectivity. Therefore, cyclodextrin chemistry is currently a significant topic in supramolecular chemistry. The more open secondary hydroxyl side of CDs is stated to be catalytically very important, modifications of this face are believed to produce valuable derivatives for catalysis, enzyme mimic, chiral discrimination, etc. Mono-6-O-(substituted benzoyl)-β-CDs as novel supramolecular photosensitizing hosts have recently excited considerable attention in photochirogenesis. The supramolecular photosenstization of cis-cyclooctene mediated by them gave chiral trans-cyclooctene, enantiomeric excess of which was critically affected by the substituent introduced to the sensitizer moiety. In order to enhance the photoenantiodifferentiating ability, and elucidate the origin mechanisms of substituent-dependent enantioselectivity, in this work a series of mono-6-O-(substituted benzoyl)-β-CDs have been synthesized, and applied for enantiodifferentiating photoisomerization of cis-cyclooctene. The major contents are as follows: 1. The general aspects of supramolecular chemistry were descibed briefly. The new progress and important achievements on methods of selective modification of cyclodextrin and supramolecular enantiodifferentiating photoisomerization of cis-cyclooctene were reviewed. 2. Twelve mono-6-O-(substituted benzoyl)-β-CDs including ten novel compounds have been synthesized. Their structures have been characterized by using UV-vis, IR, NMR and MS methods. 3. A new convenient strategy for direct acylation of β-cyclodextrin on the secondary hydroxyl face was achieved by using the combination of N-benzoylimidazole and carbonate buffer in DMF, and the acyl migration between the C-2 and C-3 hydroxyl groups of β-cyclodextrin was found. 4. Experiments using mono-6-O-(substituted benzoyl)-β-CDs as chiral sensitizing hosts for mediating the enantiodifferentiating photoisomerization of cis-cyclooctene, were carried out. The results indicate that enantiomeric excess was critically affected, or even switched in sign, by the substituent introduced to the sensitizer moiety, and polarity of solvent. Using mono-6-O-(3-methoxybenzoyl)-β-CD as chiral sensitizing host, (R)-trans-cyclooctene was obtained in up to 45.8% enantiomeric excess, which is the highest value ever reported for supramolecular photochirogenesis with analogous hosts. 5. The conformational variation of these modified CDs and their complexation behaviors with cis-cyclooctene were examined by circular dichroism spectroscopy in water-methanol mixed solvents, which reveal that the orientation of chromophore was highly sensitive to the type, position and length of the introduced substituents. In the end, the complex stability constants(Ks) were calculated, and the mechanisms of reaction were discussed. Maybe, electronic effects are more important than positions of substituents for mediating the enantiodifferentiating photoisomerization of cis-cyclooctene.

Recent developments in intelligent biomedical polymers

Intelligent polymers or stimuli-responsive polymers may exhibit distinct transitions in physical-chemical properties, including conformation, polarity, phase structure and chemical composition in response to changes in environmental stimuli. Due to their unique 'intelligent' characteristics, stimuli-sensitive polymers have found a wide variety of applications in biomedical and nanotechnological fields. This review focuses on the recent developments in biomedical application of intelligent polymer systems, such as intelligent hydrogel systems, intelligent drug delivery systems and intelligent molecular recognition systems. Also, the possible future directions for the application of these intelligent polymer systems in the biomedical field are presented.