基于氧化石墨烯的Ag~+与核酸中C-C碱基错配的相互作用研究

基于氧化石墨烯,以修饰了荧光分子的单链DNA为探针,利用荧光光谱和圆二色光谱研究了Ag+对双螺旋DNA中C-C碱基错配特异性识别,并建立了检测Ag+的荧光方法。荧光光谱表明Ag+能与带C-C错配碱基的双螺旋DNA作用,使原本被氧化石墨烯淬灭的标记在DNA上的荧光分子的荧光得到恢复。圆二色光谱表明Ag+能与双螺旋DNA中的C-C碱基错配相互作用,形成更稳定的C-Ag+-C结构。在最佳实验条件下,体系荧光强度的变化与Ag+的浓度在30.0~250.0 nmol/L之间呈良好的线性关系,方法检出限为19.1 nmol/L。为研究Ag+与核酸分子的相互作用及其在环境中对生物分子的影响等方面提供了重要依据。     

基于氧化石墨烯识别特定双螺旋DNA

依据三螺旋DNA的形成,以氧化石墨烯为基础建立了一种识别特定序列双螺旋DNA的方法。单链探针DNA能够通过静电引力作用吸附在氧化石墨烯表面,标记在单链DNA末端的荧光探针分子TAMRA由于荧光能量共振转移作用使得其荧光发生淬灭。加入目标双螺旋DNA后,单链探针DNA与目标DNA分子形成三螺旋DNA,探针DNA从氧化石墨烯表面脱附,标记在探针DNA上的荧光分子的荧光恢复。在最佳实验条件下,荧光恢复的强度与探针DNA的浓度在20.0～300.0 nmol/L具有良好的线性关系,检出限为16.9 nmol/L。该方法在DNA药物筛选及基因疾病的诊断方面具有一定的应用前景。     

以2-氨基嘌呤为荧光探针研究双链DNA分子内电荷传递机理

2-氨基嘌呤(2Ap)是腺嘌呤的结构类似物, 经常作为荧光探针分子用以研究DNA分子内电荷传递过程. 设计并合成了一系列2-氨基嘌呤和鸟嘌呤核苷酸重复序列GGG之间不同距离的双链DNA分子, 利用时间分辨荧光光谱手段研究了2Ap的荧光衰减动力学以及给体(…GGG…)与受体(2Ap)间的桥体(I, 次黄嘌呤)长度变化对双链DNA电荷传递过程的影响. 结果表明, DNA分子的荧光探针分子2-氨基嘌呤的荧光动力学呈三指数衰减. 其中几百皮秒的组分来源于2-氨基嘌呤和鸟嘌呤之间的电荷转移反应, 当两者间的距离不大于2.4 nm时, 衰减速率随距离的指数函数而减小, 衰减因子b值为1.3 nm^−1; 当两者间的距离大于2.4 nm时, 荧光衰减速率随距离增加而加快, 说明电荷转移过程还与桥体次黄嘌呤I的多重复序列能量匹配有关.     

水样中铅离子含量的测定——介绍一个分析化学研究型教学实验

介绍以结晶紫为荧光探针、凝血酶核酸适体为分子识别探针,测定水样中铅离子含量的研究型教学实验。讨论了测试体系的酸度、核酸探针与荧光探针的浓度比及其他金属离子对测定结果的影响。     

含芘荧光化学敏感器化合物同小牛胸腺DNA分子间的相互作用

研究了含芘荧光化学敏感器分子被ctDNA猝灭的荧光光谱.ctDNA分子对该化学敏感器中芘的激发单体,激基缔合物都有猝灭作用.对激发单体的猝灭速度顺序为;化合物(2)>化合物(1)>芘丁酸>化合物(3);对激基缔合物的猝灭速度顺序为;化合物(2)化合物(3).由得到的荧光猝灭数据,可按公式(2)求得荧光化学敏感器分子与ctDNA分子相互作用的稳定常数.发现化合物(2)与ctDNA分子间有着最强的相互作用能力.按ctDNA和含芘荧光化学敏感器的分子结构、构型以及分子内原子-原子的间距等提出了ctDNA分子与该荧光化学敏感器的作用模型,并对上述结果进行了初步解释.     

水溶性碳纳米粒子的制备及其在DNA和单核苷酸多态性分析中的应用

利用电化学氧化的方法制备了水溶性好、粒径为7～12nm的碳纳米粒子,该碳纳米粒子通过π-π相互作用吸附荧光标记的单链DNA探针,并能有效地猝灭其荧光．当单链DNA探针与匹配的DNA目标分子杂交形成双链DNA时,猝灭的荧光被恢复,由此可以检测1-200nmol／L的DNA目标分子。此外,在碳纳米粒子存在时,由荧光标记的DNA探针和DNA目标分子形成的双链DNA的熔解温度可以简便地被测定,当双链DNA有错配碱基时,其熔解温度降低,由此可方便、快速地分析单核苷酸多态性．     

光谱法研究对氨基苯乙酮缩对二甲氨基苯甲酰腙与DNA的相互作用

合成了对氨基苯乙酮缩对二甲氨基苯甲酰腙(AAPABH),采用荧光光谱法和UV-Vis吸收光谱法研究了AAPABH与DNA的相互作用。在pH 7.4Tris-HCl缓冲溶液中,以345 nm激发该化合物发射弱荧光,加入DNA后出现明显的荧光增强现象,表明探针分子与DNA结合形成了稳定配合物,其结合常数为5.48×107L/mol。研究了离子强度对体系荧光强度的影响,结果显示NaCl的加入未引起AAPABH-DNA体系荧光强度明显变化,表明AAPABH和DNA间不存在静电作用;同时DNA对AAPABH吸收光谱的影响表现为减色效应、探针分子与热变性后的DNA作用力明显小于与未变性DNA间的作用力、探针分子与溴化乙锭(EB)竞争结合DNA使得EB-DNA体系荧光猝灭,上述实验结果均表明探针分子主要以嵌插作用方式与DNA作用。     

寡聚酰胺PyPyPyβDp与DNA相互作用的荧光动力学

通过稳态吸收光谱、荧光光谱和时间分辨荧光光谱对寡聚酰胺分子PyPyPy(Dp(简称PPP)的光物理性质进行了详细研究. 发现PPP的激发态性质受溶剂环境影响较大, 在TKMC缓冲液中, PPP有较弱的荧光, 其荧光寿命为16 ps; 随着溶剂极性逐渐降低, 荧光光谱蓝移, 荧光强度增加, 相应荧光寿命增长. 通过对PPP与DNA双螺旋分子相互作用的荧光动力学研究表明, PPP与DNA相互作用后, 荧光强度增强, 荧光寿命从16 ps增加到32 ps, 证实了存在PPP与双螺旋DNA的结合相互作用.     

寡聚酰胺PyPyPybDp与DNA相互作用的荧光动力学

通过稳态吸收光谱、荧光光谱和时间分辨荧光光谱对寡聚酰胺分子PyPyPybDp(简称PPP)的光物理性质进行了详细研究. 发现PPP的激发态性质受溶剂环境影响较大, 在TKMC缓冲液中, PPP有较弱的荧光, 其荧光寿命为16 ps; 随着溶剂极性逐渐降低, 荧光光谱蓝移, 荧光强度增加, 相应荧光寿命增长. 通过对PPP与DNA双螺旋分子相互作用的荧光动力学研究表明, PPP与DNA相互作用后, 荧光强度增强, 荧光寿命从16 ps增加到32 ps, 证实了存在PPP与双螺旋DNA的结合相互作用.     

双链DNA分子内电荷转移超交换机理

设计并合成了一系列寡聚核苷酸组成的双链DNA分子,通过检测样品中二氨基嘌呤(Ap)荧光峰强度和相对荧光量子产率来研究DNA分子内电荷转移.实验中直接分辨和观测到双链DNA分子内电荷转移超交换机理,超交换机理在近距离起作用；而电荷转移跳跃机理,可能是通过极子运动形式体现.     

Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons

A new class of molecular beacons were developed in which pyrene fluorophores were connected both at 3' and 5' ends of a single-stranded oligonucleotide. The two pyrene-based fluorophores were synthesized from the same starting material, so that the preparation of the beacons was simplified. The detection strategy of the beacons for target DNAs is based on "excimer-monomer emission switching" of the pyrene fluorophores: excimer emission of the pyrene moieties changed to monomer one when the beacons hybridized with the targets. This type of two-state mode of fluorescence allows unambiguous detection of the target DNAs because strict 1:1 correlation between the nonhybridized and the hybridized beacons can be monitored by the presence of isoemissive points of the fluorescence changes. The beacons can detect target 19-mer DNAs and can discriminate the targets from their single-nucleotide mismatches at 1 nM concentration. Advantages of the excimer-monomer switching molecular beacons were discussed in comparison with conventional ones.     

Surface-enhanced Raman nanoparticle beacons based on bioconjugated gold nanocrystals and long range plasmonic coupling

We have developed a new class of surface-enhanced Raman scattering beacons (SERS beacons) that can be turned on and off by long-range plasmonic coupling, induced by biomolecular recognition and binding events. The beacons are based on colloidal gold nanocrystals in two sizes (40 and 60 nm) and are prepared by spectral encoding with a Raman reporter molecule, functionalized with thiolated DNA probes, and stabilized and protected by low molecular weight poly(ethylene glycol)s (PEGs). The results show the SERS signal intensities increase by 40-200-fold when the nanoparticle beacons are activated by plasmonic coupling, much higher than the bright-to-dark intensity ratios reported for traditional molecular beacons. Multivalent gold nanoparticles also have exquisite specificity and are able to recognize single-base mismatches or mutations. This class of SERS nanoparticle beacons has novel mechanisms for molecular detection and signal amplification, and its long-range coupling nature raises new opportunities in developing plasmonic probes to detect proteins, cells, and intact viruses.     

TaqMan-分子灯标：一种新型的荧光基因检测探针

在TaqMan及分子灯标的基础上开发了一类新型的均相荧光检测探针—— TaqMan-分子灯标(TaqMan-MB)，该探针集合了分子灯标的发夹结构及TaqMan探针降 解作用的工作原理，使检测效果更好．与实时PCR仪联用，可用于靶基因的定量检 测．     

Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets

Molecular beacons are sensitive fluorescent probes hybridizing selectively to designated DNA and RNA targets. They have recently become practical tools for quantitative real-time monitoring of single-stranded nucleic acids. Here, we comparatively study the performance of a variety of such probes, stemless and stem-containing DNA and PNA (peptide nucleic acid) beacons, in Tris-buffer solutions containing various concentrations of NaCl and MgCl(2). We demonstrate that different molecular beacons respond differently to the change of salt concentration, which could be attributed to the differences in their backbones and constructions. We have found that the stemless PNA beacon hybridizes rapidly to the complementary oligodeoxynucleotide and is less sensitive than the DNA beacons to the change of salt thus allowing effective detection of nucleic acid targets under various conditions. Though we found stemless DNA beacons improper for diagnostic purposes due to high background fluorescence, we believe that use of these DNA and similar RNA constructs in molecular-biophysical studies may be helpful for analysis of conformational flexibility of single-stranded nucleic acids. With the aid of PNA "openers", molecular beacons were employed for the detection of a chosen target sequence directly in double-stranded DNA (dsDNA). Conditions are found where the stemless PNA beacon strongly discriminates the complementary versus mismatched dsDNA targets. Together with the insensitivity of PNA beacons to the presence of salt and DNA-binding/processing proteins, the latter results demonstrate the potential of these probes as robust tools for recognition of specific sequences within dsDNA without denaturation and deproteinization of duplex DNA.     

Specific and Direct Amplified Detection of MicroRNA with MicroRNA:Argonaute‐2 Cleavage (miRACle) Beacons

MicroRNA detection is a valuable method for determining cell identity. Molecular beacons are elegant sensors that can transform intracellular microRNA concentration into a fluorescence intensity. While target binding enhances beacon fluorescence, the degree of enhancement is insufficient for demanding applications. The addition of specialty nucleases can enable target recycling and signal amplification, but this process complicates the assay. We have developed and characterized a class of beacons that are susceptible to the endogenous nuclease Argonaute‐2 (Ago2). After purification of the complex by co‐immunoprecipitation, microRNA:Ago2 cleavage (miRACle) beacons undergo site‐ and sequence‐specific cleavage, and show a 13‐fold fluorescence enhancement over traditional beacons. The system can be adapted to any microRNA sequence, and can cleave nuclease‐resistant, non‐RNA bases, potentially allowing miRACle beacons to be designed for cells without interference from non‐specific nucleases.     

A modified molecular beacon combining the properties of TaqMan probe

A modified molecular beacon that possesses a stem-hairpin structure as seen in conventional molecular beacons and can be cleaved during PCR in designed, and it can specifically recognize the presence of the target and was obviously more sensitive than conventional molecular beacons.     

Advanced Photosensitizer Activation Strategies for Smarter Photodynamic Therapy Beacons

Photodynamic therapy (PDT) is a clinical treatment in which a light‐absorbing drug called a photosensitizer (PS) is combined with light and molecular oxygen to generate cytotoxic singlet oxygen. PDT provides additional tissue selectivity compared to conventional chemotherapy as singlet oxygen is generated only in areas in which PS accumulates and that are simultaneously illuminated by a light source with sufficient irradiance and dose. Early PDT beacons built on this concept by adding an analyte‐responsive element that simultaneously turns on PDT and fluorescence, providing both an additional layer of selectivity and real‐time feedback of the PS′s activation state. More recent PDT beacons have expanded this idea, with new methods now available for sensing analytes, generating singlet oxygen, and reporting treatment status. In this Minireview, we consider developments in advanced activation strategies implemented in therapeutic and theranostic beacons.     

Molecular beacons: a novel DNA probe for nucleic acid and protein studies

A new concept has been introduced for molecular beacon DNA molecules. Molecular beacons are a new class of oligonucleotides that can report the presence of specific nucleic acids in both homogeneous solutions and at the liquid-solid interface. They emit an intense fluorescent signal only when hybridized to their target DNA or RNA molecules. Biotinylated molecular beacons have been designed and used for the development of ultrasensitive DNA sensors and for DNA molecular interaction studies at a solid-liquid interface. Molecular beacons have also been used to study protein-DNA interactions. They have provided a variety of exciting opportunities in DNA/RNA/protein studies.     

Chimeric peptide beacons: a direct polypeptide analog of DNA molecular beacons

We have developed a new biosensor architecture, which is comprised of a polypeptide-peptide nucleic acid tri-block copolymer and which we have termed chimeric peptide beacons (CPB), that generates an optical output via a mechanism analogous to that employed in DNA-based molecular beacons.     

Monitoring mRNA in living cells in a 3D in vitro model using TAT-peptide linked molecular beacons

There is a growing need for the development of in vitro 3D cell culture models for assessing newer therapeutics for clinical applications and mechanisms of human pathology. Molecular beacons have been successfully delivered in two-dimensional (2D) systems to monitor, detect, and localize specific mRNA expression in living cells at the single cell level. However, to date the use of molecular beacons in three-dimensional (3D) systems has not been reported. To translate this technology into specific clinical targeted applications, it is critical to develop and demonstrate efficacy in a 3D system. For the first time the use of TAT-peptide conjugated molecular beacons to monitor mRNA in a 3D in vitro system has been reported.