EpCAM aptamer-mediated survivin silencing sensitized cancer stem cells to doxorubicin in a breast cancer model

Understanding the molecular basis of drug resistance and utilising this information to overcome chemoresistance remains a key challenge in oncology. Here we report that survivin, a key protein implicated in drug resistance, is overexpressed in cancer stem cell pool of doxorubicin-resistant breast cancer cells. Moreover, by utilising an active targeting system consisting of an RNA aptamer targeted against the epithelial cell adhesion molecule and a Dicer substrate survivin siRNA, we could deliver a high dose of the siRNA to cancer stem cells in xenograft tumours. Importantly, silencing of survivin with this aptamer-siRNA chimera in cancer stem cell population led to the reversal of chemoresistance, such that combined treatment with low dose of doxorubicin inhibited stemness, eliminated cancer stem cells via apoptosis, suppressed tumour growth, and prolonged survival in mice bearing chemoresistant tumours. This strategy for in vivo cancer stem cell targeting has wide application for future effective silencing of anti-death genes and in fact any dysregulated genes involved in chemoresistance and tumour relapse.

Endothelial-cell-binding aptamer for coating of intracoronary stents

Oligonucleotides capturing CD31 endothelial cells (= aptamer) were used for coating of intracoronary stents to improve endothelialization and vascular healing.

Protein synthesis editing by a DNA aptamer.

Potential errors in decoding genetic information are corrected by tRNA-dependent amino acid recognition processes manifested through editing reactions. One example is the rejection of difficult-to-discriminate misactivated amino acids by tRNA synthetases through hydrolytic reactions. Although several crystal structures of tRNA synthetases and synthetase-tRNA complexes exist, none of them have provided insight into the editing reactions. Other work suggested that editing required active amino acid acceptor hydroxyl groups at the 3' end of a tRNA effector. We describe here the isolation of a DNA aptamer that specifically induced hydrolysis of a misactivated amino acid bound to a tRNA synthetase. The aptamer had no effect on the stability of the correctly activated amino acid and was almost as efficient as the tRNA for inducing editing activity. The aptamer has no sequence similarity to that of the tRNA effector and cannot be folded into a tRNA-like structure. These and additional data show that active acceptor hydroxyl groups in a tRNA effector and a tRNA-like structure are not essential for editing. Thus, specific bases in a nucleic acid effector trigger the editing response.

Aptamer-based surface plasmon sensor for thrombin detection

A series of surface plasmonic fibre devices were fabricated using multiple coatings deposited on a lapped section of a single mode fibre and post-fabrication UV laser irradiation processing with a phase mask, producing a surface relief grating structure. These devices showed high spectral sensitivity in the aqueous index regime ranging up to 4000 nm/RIU for wavelength and 800 dB/RIU for intensity. The devices were then coated with human thrombin binding aptamer. Several concentrations of thrombin in buffer solution were made, ranging from 1nM to 1µM. All the concentrations were detectable by the devices demonstrating that sub-nM concentrations may be monitored.

Efficient HIV-1 inhibition by a 16 nt-long RNA aptamer designed by combining in vitro selection and in silico optimisation strategies

The human immunodeficiency virus type-1 (HIV-1) genome contains multiple, highly conserved structural RNA domains that play key roles in essential viral processes. Interference with the function of these RNA domains either by disrupting their structures or by blocking their interaction with viral or cellular factors may seriously compromise HIV-1 viability. RNA aptamers are amongst the most promising synthetic molecules able to interact with structural domains of viral genomes. However, aptamer shortening up to their minimal active domain is usually necessary for scaling up production, what requires very time-consuming, trial-and-error approaches. Here we report on the in vitro selection of 64 nt-long specific aptamers against the complete 5' -untranslated region of HIV-1 genome, which inhibit more than 75% of HIV-1 production in a human cell line. The analysis of the selected sequences and structures allowed for the identification of a highly conserved 16 nt-long stem-loop motif containing a common 8 nt-long apical loop. Based on this result, an in silico designed 16 nt-long RNA aptamer, termed RNApt16, was synthesized, with sequence 5'-CCCCGGCAAGGAGGGG-3-'. The HIV-1 inhibition efficiency of such an aptamer was close to 85%, thus constituting the shortest RNA molecule so far described that efficiently interferes with HIV-1 replication.

Probing the biophysical interaction between Neocarzinostatin toxin and EpCAM RNA aptamer

Neocarzinostatin (NCS) a potent DNA-damaging, anti-tumor toxin extracted from Streptomyces carzinostaticus that recognizes double-stranded DNA bulge and induces DNA damage. 2 Fluoro (2F) Modified EpCAM RNA aptamer is a 23-mer that targets EpCAM protein, expressed on the surface of epithelial tumor cells. Understanding the interaction between NCS and the ligand is important for carrying out the targeted tumor therapy. In this study, we have investigated the biophysical interactions between NCS and 2-fluro Modified EpCAM RNA aptamer using Circular Dichroism (CD) and Infra-Red (IR) spectroscopy. The aromatic amino acid residues spanning the β sheets of NCS are found to participate in intermolecular interactions with 2 F Modified EpCAM RNA aptamer. In-silico modeling and simulation studies corroborate with CD spectra data. Furthermore, it reinforces the involvement of C and D1 strand of NCS in intermolecular interactions with EpCAM RNA aptamer. This the first report on interactions involved in the stabilization of NCS-EpCAM aptamer complex and will aid in the development of therapeutic modalities towards targeted cancer therapy.

Targeting cancer cells using LNA-modified aptamer-siRNA chimeras

Aptamers are chimerized with drug or antisense oligos or nanoparticles to generate targeted therapeutics for cancer. Aptamer chimerized siRNA rescues nonspecific delivery and, thereby, enhances the availability of siRNA to target cells. EpCAM RNA aptamer (EpApt or Ep) has potential for siRNA chimerization due to its secondary structure. Stathmin and survivin proteins are reported to aid oncogenicity in retinoblastoma (RB), breast cancer and other cancers. Thus, chimerization of EpCAM Apt with siRNA against survivin and stathmin, respectively, was performed by incorporating Locked Nucleic Acid (LNA) modification. The LNA-modified chimeric aptamers were stable until 96 h and got internalized into RB, WERI-Rb1 and breast cancer, MDAMB453 cell lines. The constructs were studied using the recombinant dicer enzyme for the siRNA generation. Quantitative polymerase chain reaction and immunofluorescence by microscopic analysis of chimeras in vitro exhibited silencing of stathmin and survivin in the RB and breast cancer model. The chimeric constructs showed significant inhibition of cell proliferation of breast cancer cells. Thus, LNA-modified aptamer-based siRNA delivery aids in cell targeting and necessitates further studies in animal models.

Truncation and mutation of a transferrin receptor aptamer enhance binding affinity

Aptamers are proving their utility in a number of applications. However, to be easily functionalized, their structure needs to be simplified. Therefore, we sought to truncate a 50-nucleotide aptamer specific to the transferrin receptor to its smallest functional unit using rational engineering of the predicted two-dimensional structure of the longer parent sequence. In addition, mutations were introduced into the binding loop to determine their effect on the selectivity of the aptamers. These base mutations enhanced the binding affinity of the aptamer, while retaining its specificity. The equilibrium dissociation constant (Kd) was reduced sixfold following the substitution of all four bases in the binding region. In addition, these aptamers were efficiently internalized into transferrin receptor-positive cells in a similar manner to the transferrin receptor antibody and demonstrated colocalization with this antibody. This study has shown that the smallest functional unit of this aptamer was 14 nucleotides. This small size will be advantageous for future applications, such as drug delivery or functionalization of other therapeutic modalities.

Targeting CD44, ABCG2 and CD133 markers using aptamers: in silico analysis of CD133 extracellular domain 2 and its aptamer

The application of nucleic acid aptamers for the diagnosis and therapy of cancer stem cells (CSCs) is expanding. The current study truncated and probed various existing aptamers against CSC markers CD44, ABCG2 and CD133 in retinoblastoma (RB) primary cells, cell lines, a breast cancer cell line and MCF7-sphere. Truncated CD44 aptamer retained its specific binding to cancer cells, ABCG2+ve MCF7-spheres and CD133+ve RB cells. Similarly, ABCG2 and CD133 aptamers showed higher affinity to ABCG2+ve, CD133+ve cells than the negative population and cell lines. All aptamers appreciably reduced viability of up to 50% and 32% of the primary RB tumor cells and cell lines, respectively. Colony formation of MCF7, RB cell lines and MCF7-sphere growth were inhibited significantly. Structure prediction, simulation of CD133 extracellular domain 2 (ExD2) and A15 followed by docking to comprehend the potential interaction revealed hydrogen bonds and non bonded interactions between them. This information could be used to improve the A15 aptamer to gain more interactions with CD133. Thus approaches undertaken here can be applied universally for cell-specific targeting, and the aptamers studied against CSC markers deserve further in vivo studies.

Aptamer-mediated siRNA delivery to target colon cancer stem cells

Cancer stem cells are often referred to as the root of cancer as they drive tumour growth and are resistant to traditional anti-cancer therapies. By using a colon cancer model, targeting the cancer stem cells with aptamers can efficiently kill these cells and prevent tumours from regrowing.

Reproducible and label-free biosensor for the selective extraction and rapid detection of proteins in biological fluids

Erythropoietin (EPO), a glycoprotein hormone of ∼34 kDa, is an important hematopoietic growth factor, mainly produced in the kidney and controls the number of red blood cells circulating in the blood stream. Sensitive and rapid recombinant human EPO (rHuEPO) detection tools that improve on the current laborious EPO detection techniques are in high demand for both clinical and sports industry. A sensitive aptamer-functionalized biosensor (aptasensor) has been developed by controlled growth of gold nanostructures (AuNS) over a gold substrate (pAu/AuNS). The aptasensor selectively binds to rHuEPO and, therefore, was used to extract and detect the drug from horse plasma by surface enhanced Raman spectroscopy (SERS). Due to the nanogap separation between the nanostructures, the high population and distribution of hot spots on the pAu/AuNS substrate surface, strong signal enhancement was acquired. By using wide area illumination (WAI) setting for the Raman detection, a low RSD of 4.92% over 150 SERS measurements was achieved. The significant reproducibility of the new biosensor addresses the serious problem of SERS signal inconsistency that hampers the use of the technique in the field. The WAI setting is compatible with handheld Raman devices. Therefore, the new aptasensor can be used for the selective extraction of rHuEPO from biological fluids and subsequently screened with handheld Raman spectrometer for SERS based in-field protein detection.

电化学SPR生物传感器的研究及应用

围绕论文题目“电化学SPR生物传感器的研究及应用”，我们将SPR传感金膜同时用作电化学研究的界面，在自行组建的电化学SPR (EC-SPR)池中进行了相关的EC-SPR研究。 本论文研究工作的主要内容包括以下几个方面： 1． 发展了一种电化学薄化控制SPR金膜厚度，优化SPR信号的方法。这种方法主要是利用在较高电位下金与氯离子发生络合反应使SPR金膜表面的金部分溶解进入溶液从而达到薄化金基底的目的。通过调节溶液中氯离子的浓度和电化学扫描的次数，可以现场调控SPR基底的金膜厚度。我们用这种处理过的金膜进行了生物分子的吸附试验，结果证明了这种处理过的金膜适用于一般的SPR分析。 2． 采用湿化学镀膜法结合光刻法制备SPR金膜微阵列，拟将用于SPR成像分析。这种方法属于湿化学法制备SPR金膜微阵列，主要是在胶体金纳米粒子的自组装膜上刻蚀出金纳米粒子的微阵列，然后用湿化学法生长出合适的金微阵列。这种方法对制备条件要求比较简单，在制备纳米金微阵列的过程中腐蚀时间比较好控制，同时催化生长出新的金面。重复试验证实了这种方法能够制备出稳定的，尺寸可控的金微阵列，有望用于SPR成像系统研究生物分子相互作用。 3． 在SPR金膜表面利用电沉积法制备了超薄的壳聚糖薄膜，并将之应用于生物分子相互作用的研究。通过一步电沉积的方法制备了超薄的壳聚糖修饰的SPR金基片，并研究了几种常见蛋白与壳聚糖薄膜的非特异性作用，进一步用鼠IgG和抗鼠IgG作为一个典型的例子研究了壳聚糖修饰膜的生物相容性。试验表明壳聚糖修饰膜有好的生物相容性。 4． 首次提出利用生物催化沉积金属纳米粒子放大SPR信号测定小分子的方法。生物小分子抗坏血酸能够还原银离子，使其在金纳米表面沉积形成金属银原子。银原子的沉积将会极大地增强SPR信号，从而实现SPR光谱对小分子抗坏血酸浓度的放大测定。每次测定后，通过电化学剥脱Ag原子，SPR芯片的表面能够完全再生。同时，剥脱的银原子的量也能够被电化学测定，这也实现了抗坏血酸的间接电化学测定。 5． 结合电化学和SPR技术表征了DNA/Zr4+多层膜在金膜表面的生长过程，并研究了这种多层膜与细胞色素c的相互作用。SPR技术被用于测定 (DNA/ Zr4+)1双层中DNA单层的有效膜厚，及其表面覆盖率。利用红外反射光谱和X-射线光电子能谱表征这种多层膜的组成。通过EC-SPR方法，这种多层膜和细胞色素c的相互作用被进一步分析。结果表明这种多层膜不仅增强了细胞色素c的固定量，而且保持了细胞色素c的生物活性。 6． 利用EC-SPR技术测定了聚苯胺支撑的双层磷脂膜中的酶促反应。通过泡囊融合法在聚苯胺表面形成HRP掺杂的磷脂双层膜。这种磷脂双层膜能够很好的保存膜内的辣根过氧化酶(HRP)的活性，同时，这种膜允许质子的跨膜传输，能够提供聚苯胺和HRP在双氧水存在下反应所需的质子，实现酶促开关控制聚苯胺氧化还原态的变化，通过SPR检测这种聚苯胺膜的氧化还原态的变化，从而达到利用SPR测定酶底物小分子的目的。 7． 开展了适配子(aptamer)的EC-SPR研究。利用亚甲基兰为外在电化学探针分子，我们设计了一种简单的、可再生的电化学方法测定小分子腺苷。结果表明这种方法对腺苷的检测具有较高的灵敏性和选择性。这种设计思路有望进一步用于构建一个可再生的SPR传感器平台，用于研究适配子与蛋白质相互作用。

Amplified electrochemical aptasensor taking AuNPs based sandwich sensing platform as a model

Here, we report a sensitive amplified electrochemical impedimetric aptasensor for thrombin, a kind of serine protease that plays important role in thrombosis and haemostasis. For improving detection sensitivity, a sandwich sensing platform is fabricated, in which the thiolated aptamers are firstly immobilized on a gold substrate to capture the thrombin molecules, and then the aptamer functionalized Au nanoparticles (AuNPs) are used to amplify the impedimetric signals.

G-quadruplex-based DNAzyme for facile colorimetric detection of thrombin

Thrombin-binding aptamer is found to bind hemin to form a catalytic complex whose activity is significantly promoted by the addition of thrombin, which enables the colorimetric detection of thrombin with high specificity and sensitivity in a facile way.

DNAzyme-based Colorimetric Sensing of Lead (Pb2+) Using Unmodified Gold Nanoparticle Probes

Novel functional oligonucleotides, especially DNAzymes with RNA-cleavage activity, have been intensively studied due to their potential applications in therapeutics and sensors. Taking advantage of the high specificity of 17E DNAzyme for Pb2+, highly sensitive and selective fluorescent, electrochemical and colorimetric sensors have been developed for Pb2+. In this work, we report a simple, sensitive and label-free 17E DNAzyme-based sensor for Pb2+ detection using unmodified gold nanoparticles (GNPs) based on the fact that unfolded single-stranded DNA could be adsorbed on the citrate protected GNPs while double-stranded DNA could not. By our method the substrate cleavage by the 17E DNAzyme in the presence of Pb2+ could be monitored by color change of GNPs, thereby Pb2+ detection was realized.