基于纳米材料和功能核酸的光学传感新方法用于酶活性检测
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摘要
近年来，生物传感器因其灵敏度高、选择性好、分析时间短、检测成本低等特点，极大地推动了医学临床诊断和药物筛选的发展。光学检测技术具有操作简便、无需分离、可以实现原位和实时活体测定等优点，在建立生物传感器方面正被越来越多的研究者所关注。此外，功能核酸和纳米材料的发展为构建用于各种分析对象的生物传感技术提供了全新的设计思路和平台。本论文基于当前一些重要酶活性检测及其相关药物筛选中的研究热点，重点探讨如何提高检测灵敏度、降低检测成本等问题。将纳米材料、功能核酸的优势相结合，发展了一些光学检测新技术用于碱性磷酸酯酶、多聚核苷激酶、腺苷脱氨酶、碱基切除修复酶等酶活性及其抑制剂的测定。和传统方法相比，本论文所建立的检测方法灵敏度高、操作简便、分析成本低廉。同时还初步验证了这些方法的实用性。具体内容如下：
碱性磷酸酯酶（ALP）的测定在相关疾病的临床诊断中具有重要作用。在第2章中，基于焦磷酸（PPi）对荧光铜纳米粒子合成的抑制能力，以PPi为底物，建立了一种可在生理条件下检测ALP的无标记信号增强型方法。PPi可以和Cu2+之间形成很强的络合物，该络合作用将妨碍CuNPs的合成，造成荧光信号的降低。利用ALP对PPi的水解，使得PPi与Cu2+之间的络合不能发生。在dsDNA模板的存在下，通过抗坏血酸对Cu2+的还原，CuNPs可以被有效地合成，从而荧光恢复，并且其恢复能力和ALP浓度直接相关。该方法不需要任何标记或者复杂的设计，操作简便，分析成本低。并且该方法具有较高的灵敏度，其检测下限达到0.1nM。此外，信号增强模式也为ALP的测定提供了较好的选择性。同时，还利用所建立的方法研究了磷酸根对ALP酶活性的抑制情况。在复杂环境中，该检测方法同样表现出了良好的分析性能。血清样品中的回收率实验结果令人满意。
多聚核苷激酶（PNK）对DNA的磷酸化修饰过程在DNA损伤修复、复制和重组中起着非常重要的作用。第3章中，利用双链DNA模板法制备的荧光铜纳米粒子（CuNPs）为信号指示剂，开发了一种无标记荧光方法用于PNK酶活性的测定。实验中，利用一段双链DNA同时作为PNK的底物和CuNPs合成的模板。当PNK作用之后，双链DNA模板将被磷酸化，导致双链DNA立即被λ核酸外切酶降解。由于缺少了CuNPs合成所需的双链DNA模板，该降解过程将抑制CuNPs的形成，造成荧光信号的下降。该测定方法不需要对底物DNA进行任何化学修饰或者复杂的序列设计，从而使整个实验操作简便，成本低廉。并且该方法选择性好，灵敏度高，其检测下限为0.49U/mL。同时该检测方法在复杂体系中也具有较好的分析性能。
腺苷脱氨酶（ADA）活性的测定及其抑制剂的筛选在临床诊断中具有重要意义。第4章中，以腺苷脱氨酶为模型分析物，将氧化石墨烯对不同构象核酸吸附能力的差异和核酸适配体对目标识别的高特异性相结合，并利用SYBR green I作为荧光指示剂，构建了一种基于氧化石墨烯-适配体平台的无标记高信背比荧光生物检测方法。两条劈开的适配体片段共同对腺苷的识别形成复合结构，荧光染料将嵌入适配体/腺苷复合物的双链区域。并且复合结构的形成也妨碍适配体片段在石墨烯表面的吸附，从而溶液具有较强的荧光信号。而腺苷脱氨酶对腺苷去氨基后，生成的次黄苷不能被适配体识别，适配体和荧光染料将吸附在石墨烯表面，导致荧光淬灭。该方法无需对适配体探针进行化学修饰，易于合成制备，降低了分析成本。同时，氧化石墨烯的超强荧光淬灭能力也为该方法提供了较高的灵敏度，其检测下限为0.025U/mL。该方法为基于适配体的其他生物分子的检测提供了一个参考手段。第5章中，基于酶调控纳米金团聚策略，提出了一种无标记可视化分析方法用于腺苷脱氨酶及其抑制剂的便捷灵敏测定。该方法主要依赖于腺嘌呤碱基环外氨基与纳米金之间的强烈作用，从而置换出纳米金表面弱结合的柠檬酸根离子，降低了纳米金稳定性，最终造成纳米金的团聚。而腺苷脱氨酶对腺苷的脱氨基反应将抑制这个腺苷依赖的纳米金团聚现象。该方法无需其他辅助酶、核酸适配体或者化学修饰，使得整个测定过程简便、低成本，分析速度快，并实现了腺苷脱氨酶均相可视化检测。该方法动态范围宽，灵敏度高，其线性检测范围为0-15U/L，检测下限为0.8827U/L。此外，该方法还实现了腺苷脱氨酶抑制剂的可视化筛选测定。
碱基切除修复是DNA损伤修复过程中的重要途径之一，其修复酶活性和多种疾病相关。在第6章中，以尿嘧啶-DNA糖基化酶（UDG）为模型分析物，基于目标激活自催化DNA酶信号放大策略，建立了两种新型荧光分析方法用于碱基切除修复酶活性的测定。其基本思路是利用UDG的作用激活DNA酶，在辅助因子的存在下催化循环切割信标结构的底物探针，对目标的测定信号进行放大。首先，基于UDG作用将降低其底物的熔链温度这一特性，利用一条双链DNA底物来构建目标激活自催化DNA酶策略。UDG的作用将使得DNA酶从双链底物中释放出去，从而激活DNA酶对信标底物的催化循环切割。该方法具有较宽的动态范围和较高的灵敏度，其线性检测范围为0-1.0U/mL，检测下限为0.023U/mL。并且，该方法也被成功用于UDG的抑制剂测定。其次，将滚环放大（RCA）反应引入检测体系构建RCA辅助的自催化DNA酶策略。该方法以环状探针为UDG底物，通过核酸内切酶IV对UDG作用后产生的脱碱基位点进行切割。切割生成的核酸片段将作为引物引发RCA反应，产生大量的重复的DNA酶序列。每个新生成的DNA酶均可以对其信标底物进行循环切割。通过双重信号放大，该方法检测灵敏度显著提高，其检测下限达到0.002U/mL。
Recently, biosensors have greatly promoted the development of clinical diagnosisand drug screening, because of their high sensitivity, good selectivity, short analysistime and low-cost. Optical detection technology has attracted a great attention in theconstruction of biosensors, due to many advantages such as easy operation, noseparation and the detection can be implemented in situ, real-time and in vivo.Moreover, the development of functional nucleic acids and nanomaterials providemore novel strategies and platforms for the design of biosensing technology. Thisdoctoral thesis concerns on the research hotspot in the enzyme activity detection anddrug screening, focusing on how to improve the sensitivity, reduce the cost and so on.Combination of the advantages of nanomaterials and functional nucleic acids, severaloptical detection methods have been developed for the detection of alkalinephosphatase, polynucleotide kinase,adenosine deaminase, base excision repair enzymeand their inhibitors. Compared with the traditional methods, the proposed detectionmethods are sensitive, convenient and cost-effective. The practicability of thesedeveloped methods was also verified. The detailed contents are described as follows.
Alkaline phosphatase (ALP) plays an important role in the clinical diagnosis ofrelated diseases. In chapter2, based on the inhibition of the synthesis of dsDNA-templated fluorescent copper nanoparticles (CuNPs) by pyrophosphate (PPi), a novellabel free turn-on fluorescent strategy for detecting ALP under physiologicalconditions has been developed using PPi substrate. This method relies on the stronginteraction between PPi and Cu2+, which would hamper the effective formation offluorescent CuNPs, leading to low fluorescence intensity. The ALP-catalyzed PPihydrolysis would disable the complexation between Cu2+and PPi, facilitating theformation of fluorescent CuNPs through the reduction by ascorbate in the presence ofdsDNA templates. Thus the fluorescence intensity was recovered and the fluorescenceenhancement was related to the concentration of ALP. This method is cost-effectiveand convenient without any labels or complicated operations. The present strategyexhibits a high sensitivity with a detection limit of0.1nM. The turn-on mode alsoprovides a high selectivity for ALP assay. Additionally, the inhibition effect ofphosphate on ALP activity was also studied. It also exhibited a good assayperformance in complex samples and satisfactory recoveries in diluted serum samples were obtained.
Phosphorylation of DNA by polynucleotide kinase (PNK) is important in DNAdamage repair, replication and recombination. The evaluation of PNK activity hasreceived an increasing attention due to the significance of PNK. In chapter3, wepresented a label free fluorescent method for PNK activity assay using double strandDNA (dsDNA)-templated copper nanoparticles (CuNPs) as a fluorescent indicator. AdsDNA probe was introduced to act as both enzyme’s substrate and template forCuNPs formation. Upon the PNK reaction, the dsDNA template was phosphorylatedand then digested by λ exonuclease immediately, prohibiting the formation offluorescent CuNPs due to the lack of dsDNA template. This homogeneous PNKactivity assay does not require any other additional modifications of DNA substrate orcomplex design, making the proposed strategy simple, cost-effective and highthroughput. The proposed strategy is selective and sensitive with a detection limit of0.49U/mL. It also worked well in complex biological samples.
The evaluation of adenosine deaminase (ADA) activity and its inhibitors takes animportant part in clinical diagnostics and drug screening. In chapter4, combination ofthe high specificity of aptamer and different adsorption ability of graphene oxide fornucleic acids with different conformation, using SYBR green I as an indicator andadenosine deaminase (ADA) as a model analyte, a label free fluorescent biologicaldetection method was designed based on the graphene oxide–aptamer platform. Twoparts of split aptamer can specifically recognize adenosine together, SYBR green Icould then stained in the duplex region of the aptamer/adenosine complex. Theformation of aptamer/adenosine complex made the aptamer to be released form thesurface of graphene oxide, resulting in a high fluorescence signal. After thedeamination of adenosine by ADA, the aptamer could not recognize the productinosine, and the aptamer and fluorescence dye were adsorbed on the surface ofgraphene oxide, leading to the fluorescence quenching. This method did not requirechemical modification on aptamer probes, making the analysis costless. Additionally, ahigher sensitivity was also obtained due to the strong fluorescence quenching ability. Italso provided a usefull technology for the detection other biomolecules usingaptamer-based methods. In chapter5, a novel label free colorimetric assay has beendeveloped for convenient and sensitive detection of ADA activity and its inhibitorbased on the enzyme-regulated aggregation of unmodified gold nanoparticles (AuNPs).This strategy relied on the strong interaction between exocyclic amino group ofadenosine and AuNPs which could diminish the stability of citrate-capped AuNPs by the displacement of citrate ions from the AuNPs surface, resulting in the aggregation.The deamination of adenosine by ADA prohibited the adenosine-dependentaggregation. This enzyme-regulated-aggregation strategy allowed a visual andhomogeneous assay of ADA activity without any other coupling enzymes, aptamers oradditional modifications, making the proposed strategy simple, cost-effective and highthroughput. The present strategy is highly selective and sensitive for ADA assay with adetection limit of0.8227U/L. Moreover, the evaluation of inhibition for ADA activityusing this colorimetric method was also successfully demonstrated.
The base excision repair (BER) pathway plays a key role in resisting DNA lesions,and the activity of BER enzyme is connected to several diseases. In chapter6, usinguracil-DNA glycosylase (UDG) as a model analyte, two novel fluorescent methodswere developed for the detection of the BER enzyme based on the autocatalyticDNAzyme amplification strategy. UDG reaction could activate the DNAzyme whichcatalyzed the cycling cleavage of a molecular beacon (MB) structured probe in thepresence of cofactor, resulting in signal amplification in the detection of UDG activity.First, based on the decrease of melting temperature of substrate upon UDG reaction, adouble-stranded substrate was used to demonstrate this target-activated autocatalyticDNAzyme amplification strategy. DNAzyme was released from the double-strandedsubstrate after the treatment by UDG. The released DNAzyme could then catalyze thecycling cleavage of MB substrate. The present method exhibits a wide dynamic rangeand a high sensitivity, with a linear detection range from0to1.0U/mL and a detectionlimit of0.023U/mL. Additionally, this method could also be applied to evaluate theinhibition of UDG. Second, a rolling circle amplification (RCA) process wasincorporated into the DNAzyme strategy. This RCA-assisted CAMB strategy relied onthe digest of abasic site generated by UDG treatment using endonuclease IV. Thiscleavage produced a new primer probe with3′hydroxyl end that could initiate a linearRCA reaction. The RCA product had a tandem repeated sequence of DNAzyme, andeach DNAzyme sequence could cyclically cleave the MB probe and generated anincreased fluorescence signal. A remarkable enhancement of sensitivity (limit ofdetection=0.002U/mL) is obtained due to the coupled signal amplification cascade.
碱性磷酸酯酶（ALP）的测定在相关疾病的临床诊断中具有重要作用。在第2章中，基于焦磷酸（PPi）对荧光铜纳米粒子合成的抑制能力，以PPi为底物，建立了一种可在生理条件下检测ALP的无标记信号增强型方法。PPi可以和Cu2+之间形成很强的络合物，该络合作用将妨碍CuNPs的合成，造成荧光信号的降低。利用ALP对PPi的水解，使得PPi与Cu2+之间的络合不能发生。在dsDNA模板的存在下，通过抗坏血酸对Cu2+的还原，CuNPs可以被有效地合成，从而荧光恢复，并且其恢复能力和ALP浓度直接相关。该方法不需要任何标记或者复杂的设计，操作简便，分析成本低。并且该方法具有较高的灵敏度，其检测下限达到0.1nM。此外，信号增强模式也为ALP的测定提供了较好的选择性。同时，还利用所建立的方法研究了磷酸根对ALP酶活性的抑制情况。在复杂环境中，该检测方法同样表现出了良好的分析性能。血清样品中的回收率实验结果令人满意。
多聚核苷激酶（PNK）对DNA的磷酸化修饰过程在DNA损伤修复、复制和重组中起着非常重要的作用。第3章中，利用双链DNA模板法制备的荧光铜纳米粒子（CuNPs）为信号指示剂，开发了一种无标记荧光方法用于PNK酶活性的测定。实验中，利用一段双链DNA同时作为PNK的底物和CuNPs合成的模板。当PNK作用之后，双链DNA模板将被磷酸化，导致双链DNA立即被λ核酸外切酶降解。由于缺少了CuNPs合成所需的双链DNA模板，该降解过程将抑制CuNPs的形成，造成荧光信号的下降。该测定方法不需要对底物DNA进行任何化学修饰或者复杂的序列设计，从而使整个实验操作简便，成本低廉。并且该方法选择性好，灵敏度高，其检测下限为0.49U/mL。同时该检测方法在复杂体系中也具有较好的分析性能。
腺苷脱氨酶（ADA）活性的测定及其抑制剂的筛选在临床诊断中具有重要意义。第4章中，以腺苷脱氨酶为模型分析物，将氧化石墨烯对不同构象核酸吸附能力的差异和核酸适配体对目标识别的高特异性相结合，并利用SYBR green I作为荧光指示剂，构建了一种基于氧化石墨烯-适配体平台的无标记高信背比荧光生物检测方法。两条劈开的适配体片段共同对腺苷的识别形成复合结构，荧光染料将嵌入适配体/腺苷复合物的双链区域。并且复合结构的形成也妨碍适配体片段在石墨烯表面的吸附，从而溶液具有较强的荧光信号。而腺苷脱氨酶对腺苷去氨基后，生成的次黄苷不能被适配体识别，适配体和荧光染料将吸附在石墨烯表面，导致荧光淬灭。该方法无需对适配体探针进行化学修饰，易于合成制备，降低了分析成本。同时，氧化石墨烯的超强荧光淬灭能力也为该方法提供了较高的灵敏度，其检测下限为0.025U/mL。该方法为基于适配体的其他生物分子的检测提供了一个参考手段。第5章中，基于酶调控纳米金团聚策略，提出了一种无标记可视化分析方法用于腺苷脱氨酶及其抑制剂的便捷灵敏测定。该方法主要依赖于腺嘌呤碱基环外氨基与纳米金之间的强烈作用，从而置换出纳米金表面弱结合的柠檬酸根离子，降低了纳米金稳定性，最终造成纳米金的团聚。而腺苷脱氨酶对腺苷的脱氨基反应将抑制这个腺苷依赖的纳米金团聚现象。该方法无需其他辅助酶、核酸适配体或者化学修饰，使得整个测定过程简便、低成本，分析速度快，并实现了腺苷脱氨酶均相可视化检测。该方法动态范围宽，灵敏度高，其线性检测范围为0-15U/L，检测下限为0.8827U/L。此外，该方法还实现了腺苷脱氨酶抑制剂的可视化筛选测定。
碱基切除修复是DNA损伤修复过程中的重要途径之一，其修复酶活性和多种疾病相关。在第6章中，以尿嘧啶-DNA糖基化酶（UDG）为模型分析物，基于目标激活自催化DNA酶信号放大策略，建立了两种新型荧光分析方法用于碱基切除修复酶活性的测定。其基本思路是利用UDG的作用激活DNA酶，在辅助因子的存在下催化循环切割信标结构的底物探针，对目标的测定信号进行放大。首先，基于UDG作用将降低其底物的熔链温度这一特性，利用一条双链DNA底物来构建目标激活自催化DNA酶策略。UDG的作用将使得DNA酶从双链底物中释放出去，从而激活DNA酶对信标底物的催化循环切割。该方法具有较宽的动态范围和较高的灵敏度，其线性检测范围为0-1.0U/mL，检测下限为0.023U/mL。并且，该方法也被成功用于UDG的抑制剂测定。其次，将滚环放大（RCA）反应引入检测体系构建RCA辅助的自催化DNA酶策略。该方法以环状探针为UDG底物，通过核酸内切酶IV对UDG作用后产生的脱碱基位点进行切割。切割生成的核酸片段将作为引物引发RCA反应，产生大量的重复的DNA酶序列。每个新生成的DNA酶均可以对其信标底物进行循环切割。通过双重信号放大，该方法检测灵敏度显著提高，其检测下限达到0.002U/mL。
Recently, biosensors have greatly promoted the development of clinical diagnosisand drug screening, because of their high sensitivity, good selectivity, short analysistime and low-cost. Optical detection technology has attracted a great attention in theconstruction of biosensors, due to many advantages such as easy operation, noseparation and the detection can be implemented in situ, real-time and in vivo.Moreover, the development of functional nucleic acids and nanomaterials providemore novel strategies and platforms for the design of biosensing technology. Thisdoctoral thesis concerns on the research hotspot in the enzyme activity detection anddrug screening, focusing on how to improve the sensitivity, reduce the cost and so on.Combination of the advantages of nanomaterials and functional nucleic acids, severaloptical detection methods have been developed for the detection of alkalinephosphatase, polynucleotide kinase,adenosine deaminase, base excision repair enzymeand their inhibitors. Compared with the traditional methods, the proposed detectionmethods are sensitive, convenient and cost-effective. The practicability of thesedeveloped methods was also verified. The detailed contents are described as follows.
Alkaline phosphatase (ALP) plays an important role in the clinical diagnosis ofrelated diseases. In chapter2, based on the inhibition of the synthesis of dsDNA-templated fluorescent copper nanoparticles (CuNPs) by pyrophosphate (PPi), a novellabel free turn-on fluorescent strategy for detecting ALP under physiologicalconditions has been developed using PPi substrate. This method relies on the stronginteraction between PPi and Cu2+, which would hamper the effective formation offluorescent CuNPs, leading to low fluorescence intensity. The ALP-catalyzed PPihydrolysis would disable the complexation between Cu2+and PPi, facilitating theformation of fluorescent CuNPs through the reduction by ascorbate in the presence ofdsDNA templates. Thus the fluorescence intensity was recovered and the fluorescenceenhancement was related to the concentration of ALP. This method is cost-effectiveand convenient without any labels or complicated operations. The present strategyexhibits a high sensitivity with a detection limit of0.1nM. The turn-on mode alsoprovides a high selectivity for ALP assay. Additionally, the inhibition effect ofphosphate on ALP activity was also studied. It also exhibited a good assayperformance in complex samples and satisfactory recoveries in diluted serum samples were obtained.
Phosphorylation of DNA by polynucleotide kinase (PNK) is important in DNAdamage repair, replication and recombination. The evaluation of PNK activity hasreceived an increasing attention due to the significance of PNK. In chapter3, wepresented a label free fluorescent method for PNK activity assay using double strandDNA (dsDNA)-templated copper nanoparticles (CuNPs) as a fluorescent indicator. AdsDNA probe was introduced to act as both enzyme’s substrate and template forCuNPs formation. Upon the PNK reaction, the dsDNA template was phosphorylatedand then digested by λ exonuclease immediately, prohibiting the formation offluorescent CuNPs due to the lack of dsDNA template. This homogeneous PNKactivity assay does not require any other additional modifications of DNA substrate orcomplex design, making the proposed strategy simple, cost-effective and highthroughput. The proposed strategy is selective and sensitive with a detection limit of0.49U/mL. It also worked well in complex biological samples.
The evaluation of adenosine deaminase (ADA) activity and its inhibitors takes animportant part in clinical diagnostics and drug screening. In chapter4, combination ofthe high specificity of aptamer and different adsorption ability of graphene oxide fornucleic acids with different conformation, using SYBR green I as an indicator andadenosine deaminase (ADA) as a model analyte, a label free fluorescent biologicaldetection method was designed based on the graphene oxide–aptamer platform. Twoparts of split aptamer can specifically recognize adenosine together, SYBR green Icould then stained in the duplex region of the aptamer/adenosine complex. Theformation of aptamer/adenosine complex made the aptamer to be released form thesurface of graphene oxide, resulting in a high fluorescence signal. After thedeamination of adenosine by ADA, the aptamer could not recognize the productinosine, and the aptamer and fluorescence dye were adsorbed on the surface ofgraphene oxide, leading to the fluorescence quenching. This method did not requirechemical modification on aptamer probes, making the analysis costless. Additionally, ahigher sensitivity was also obtained due to the strong fluorescence quenching ability. Italso provided a usefull technology for the detection other biomolecules usingaptamer-based methods. In chapter5, a novel label free colorimetric assay has beendeveloped for convenient and sensitive detection of ADA activity and its inhibitorbased on the enzyme-regulated aggregation of unmodified gold nanoparticles (AuNPs).This strategy relied on the strong interaction between exocyclic amino group ofadenosine and AuNPs which could diminish the stability of citrate-capped AuNPs by the displacement of citrate ions from the AuNPs surface, resulting in the aggregation.The deamination of adenosine by ADA prohibited the adenosine-dependentaggregation. This enzyme-regulated-aggregation strategy allowed a visual andhomogeneous assay of ADA activity without any other coupling enzymes, aptamers oradditional modifications, making the proposed strategy simple, cost-effective and highthroughput. The present strategy is highly selective and sensitive for ADA assay with adetection limit of0.8227U/L. Moreover, the evaluation of inhibition for ADA activityusing this colorimetric method was also successfully demonstrated.
The base excision repair (BER) pathway plays a key role in resisting DNA lesions,and the activity of BER enzyme is connected to several diseases. In chapter6, usinguracil-DNA glycosylase (UDG) as a model analyte, two novel fluorescent methodswere developed for the detection of the BER enzyme based on the autocatalyticDNAzyme amplification strategy. UDG reaction could activate the DNAzyme whichcatalyzed the cycling cleavage of a molecular beacon (MB) structured probe in thepresence of cofactor, resulting in signal amplification in the detection of UDG activity.First, based on the decrease of melting temperature of substrate upon UDG reaction, adouble-stranded substrate was used to demonstrate this target-activated autocatalyticDNAzyme amplification strategy. DNAzyme was released from the double-strandedsubstrate after the treatment by UDG. The released DNAzyme could then catalyze thecycling cleavage of MB substrate. The present method exhibits a wide dynamic rangeand a high sensitivity, with a linear detection range from0to1.0U/mL and a detectionlimit of0.023U/mL. Additionally, this method could also be applied to evaluate theinhibition of UDG. Second, a rolling circle amplification (RCA) process wasincorporated into the DNAzyme strategy. This RCA-assisted CAMB strategy relied onthe digest of abasic site generated by UDG treatment using endonuclease IV. Thiscleavage produced a new primer probe with3′hydroxyl end that could initiate a linearRCA reaction. The RCA product had a tandem repeated sequence of DNAzyme, andeach DNAzyme sequence could cyclically cleave the MB probe and generated anincreased fluorescence signal. A remarkable enhancement of sensitivity (limit ofdetection=0.002U/mL) is obtained due to the coupled signal amplification cascade.
引文
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