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1.
Int J Mol Sci ; 22(23)2021 Nov 30.
Article in English | MEDLINE | ID: mdl-34884745

ABSTRACT

Aptamers offer a great opportunity to develop innovative drug delivery systems that can deliver cargos specifically into targeted cells. In this study, a chimera consisting of two aptamers was developed to deliver doxorubicin into cancer cells and release the drug in cytoplasm in response to adenosine-5'-triphosphate (ATP) binding. The chimera was composed of the AS1411 anti-nucleolin aptamer for cancer cell targeting and the ATP aptamer for loading and triggering the release of doxorubicin in cells. The chimera was first produced by hybridizing the ATP aptamer with its complementary DNA sequence, which is linked with the AS1411 aptamer via a poly-thymine linker. Doxorubicin was then loaded inside the hybridized DNA region of the chimera. Our results show that the AS1411-ATP aptamer chimera was able to release loaded doxorubicin in cells in response to ATP. In addition, selective uptake of the chimera into cancer cells was demonstrated using flow cytometry. Furthermore, confocal laser scanning microscopy showed the successful delivery of the doxorubicin loaded in chimeras to the nuclei of targeted cells. Moreover, the doxorubicin-loaded chimeras effectively inhibited the growth of cancer cell lines and reduced the cytotoxic effect on the normal cells. Overall, the results of this study show that the AS1411-ATP aptamer chimera could be used as an innovative approach for the selective delivery of doxorubicin to cancer cells, which may improve the therapeutic potency and decrease the off-target cytotoxicity of doxorubicin.


Subject(s)
Aptamers, Nucleotide , Doxorubicin , Drug Delivery Systems , Neoplasms , Humans , Adenosine Triphosphate/metabolism , Aptamers, Nucleotide/administration & dosage , Aptamers, Nucleotide/blood , Aptamers, Nucleotide/genetics , Cell Line, Tumor , Doxorubicin/administration & dosage , Drug Delivery Systems/methods , Drug Design , Drug Stability , In Vitro Techniques , MCF-7 Cells , Molecular Targeted Therapy , Neoplasms/drug therapy , Oligodeoxyribonucleotides/administration & dosage , Oligodeoxyribonucleotides/blood , Oligodeoxyribonucleotides/genetics , Phosphoproteins/antagonists & inhibitors , RNA-Binding Proteins/antagonists & inhibitors , Nucleolin
2.
Nucleic Acids Res ; 48(19): 10680-10690, 2020 11 04.
Article in English | MEDLINE | ID: mdl-33021630

ABSTRACT

Circular DNA aptamers are powerful candidates for therapeutic applications given their dramatically enhanced biostability. Herein we report the first effort to evolve circular DNA aptamers that bind a human protein directly in serum, a complex biofluid. Targeting human thrombin, this strategy has led to the discovery of a circular aptamer, named CTBA4T-B1, that exhibits very high binding affinity (with a dissociation constant of 19 pM), excellent anticoagulation activity (with the half maximal inhibitory concentration of 90 pM) and high stability (with a half-life of 8 h) in human serum, highlighting the advantage of performing aptamer selection directly in the environment where the application is intended. CTBA4T-B1 is predicted to adopt a unique structural fold with a central two-tiered guanine quadruplex capped by two long stem-loops. This structural arrangement differs from all known thrombin binding linear DNA aptamers, demonstrating the added advantage of evolving aptamers from circular DNA libraries. The method described here permits the derivation of circular DNA aptamers directly in biological fluids and could potentially be adapted to generate other types of aptamers for therapeutic applications.


Subject(s)
Aptamers, Nucleotide/chemistry , DNA, Circular/chemistry , Thrombin/metabolism , Aptamers, Nucleotide/blood , Aptamers, Nucleotide/metabolism , DNA, Circular/blood , DNA, Circular/metabolism , G-Quadruplexes , Humans , Protein Binding , Thrombin/chemistry
3.
Anal Chem ; 92(9): 6495-6501, 2020 05 05.
Article in English | MEDLINE | ID: mdl-32250595

ABSTRACT

The e antigen of hepatitis B (HBeAg) is positively associated with an increased risk of developing liver cancer and cirrhosis in chronic hepatitis B (CHB) patients. Clinical monitoring of HBeAg provides guidance to the treatment of CHB and the assessment of disease progression. We describe here an affinity binding assay for HBeAg, which takes advantage of G-quadruplex aptamers for enhanced binding and stability. We demonstrate a strategy to improve the binding affinity of aptamers by modifying their sequences upon their G-quadruplex and secondary structures. On the basis of predicting a stable G-quadruplex and a secondary structure, we truncated 19 nucleotides (nt) from the primer regions of an 80-nt aptamer, and the resulting 61-nt aptamer enhanced binding affinity by 19 times (Kd = 1.2 nM). We mutated a second aptamer (40 nt) in one loop region and incorporated pyrrolo-deoxycytidine to replace deoxycytidine in another loop. The modified 40-nt aptamer, with a stable G-quadruplex and two modified loops, exhibited a 100 times higher binding affinity for HBeAg (Kd = 0.4 nM) than the unmodified original aptamer. Using the two newly modified aptamers, one serving as the capture and the other as the reporter, we have developed an improved sandwich binding assay for HBeAg. Analyses of HBeAg in serum samples (concentration ranging from 0.1 to 60 ng/mL) of 10 hepatitis B patients, showing consistent results with clinical tests, demonstrate a successful application of the aptamer modification strategy and the associated aptamer binding assay.


Subject(s)
Aptamers, Nucleotide/chemistry , Hepatitis B e Antigens/chemistry , Aptamers, Nucleotide/blood , Binding Sites , G-Quadruplexes , Hepatitis B e Antigens/blood , Hepatitis B, Chronic/blood , Humans , Nucleic Acid Conformation
4.
Nucleic Acids Res ; 48(7): 3975-3986, 2020 04 17.
Article in English | MEDLINE | ID: mdl-32095808

ABSTRACT

Guanine-rich regions of the human genome can adopt non-canonical secondary structures. Their role in regulating gene expression has turned them into promising targets for therapeutic intervention. Ligands based on polyaromatic moieties are especially suitable for targeting G-quadruplexes utilizing their size complementarity to interact with the large exposed surface area of four guanine bases. A predictable way of (de)stabilizing specific G-quadruplex structures through efficient base stacking of polyaromatic functional groups could become a valuable tool in our therapeutic arsenal. We have investigated the effect of pyrene-modified uridine nucleotides incorporated at several positions of the thrombin binding aptamer (TBA) as a model system. Characterization using spectroscopic and biophysical methods provided important insights into modes of interaction between pyrene groups and the G-quadruplex core as well as (de)stabilization by enthalpic and entropic contributions. NMR data demonstrated that incorporation of pyrene group into G-rich oligonucleotide such as TBA may result in significant changes in 3D structure such as formation of novel dimeric topology. Site specific structural changes induced by stacking of the pyrene moiety on nearby nucleobases corelate with distinct thrombin binding affinities and increased resistance against nuclease degradation.


Subject(s)
Aptamers, Nucleotide/chemistry , G-Quadruplexes , Pyrenes/chemistry , Aptamers, Nucleotide/blood , Aptamers, Nucleotide/metabolism , Deoxyribonucleases , Dimerization , Entropy , Humans , Thermodynamics , Thrombin/metabolism , Uracil Nucleotides/chemistry
5.
Anal Chem ; 92(5): 4108-4114, 2020 03 03.
Article in English | MEDLINE | ID: mdl-32037790

ABSTRACT

Developing cancer targeted medicine depends on increasing delivery efficiency and tumor site accumulation of theranostic agents. To accomplish this, we report a modification of PTK7 receptor-specific aptamer Sgc8 with the small molecule Evans Blue (EB), thus implementing an albumin binding hitchhike strategy for prolonged blood circulation. The EB molecule could insert into the hydrophobic region of serum albumin and form an aptamer/albumin complex. This complex showed superior physiological stability, facilitating longer blood half-life, and maintaining its targeting capacity. Successful conjugation of EB-aptamers was confirmed by a series of characterization methods. Targeting performance was tested on a xenografted mouse tumor model. Taking advantage of the long circulating aptamer/HSA complex, improved accumulation, and delivery efficiency to the tumor site were achieved. Through ex vivo quantification of the EB-Sgc8 aptamers' biodistribution, the mechanism of improved targeting performance was illuminated. Therefore, the increased aptamers tumor delivery efficiency and accumulation indicate that prolonging blood circulation is a promising strategy to improve aptamers' targeted delivery performance in the future clinical translation.


Subject(s)
Aptamers, Nucleotide/metabolism , Neoplasms/diagnostic imaging , Animals , Aptamers, Nucleotide/blood , Aptamers, Nucleotide/chemistry , Cell Line, Tumor , Evans Blue/chemistry , Half-Life , Humans , Mice , Mice, Nude , Neoplasms/pathology , Optical Imaging , Serum Albumin/chemistry , Serum Albumin/metabolism , Tissue Distribution , Xenograft Model Antitumor Assays
6.
Nanotechnology ; 31(9): 095104, 2020 Feb 21.
Article in English | MEDLINE | ID: mdl-31726443

ABSTRACT

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the clinic, with the characteristics of occult onset, rapid progression, and high degree of malignancy. Alpha fetoprotein (AFP) is the most important biomarker of HCC, which is widely used in early screening, diagnosis, and prognosis observation. A series of immunoassays have been developed and frequently used in the detection of AFP based on antibodies. Unfortunately, the shortcomings of antibodies, such as thermal unstable and fluctuant activity by batches, lead to the inaccuracy in the detection of AFP. In this study, aptamers instead of antibodies were adopted as the specific recognition element for AFP, aiming to seek an alternative strategy to immunoassays. An AFP-specific ssDNA aptamer was grafted to magnetic nanoparticles (Fe3O4@SiO2) via avidin-biotin interaction, and the resultant aptamer functionalized magnetic nanoparticles (Ap-MNPs) were adequately characterized and tested. The Ap-MNPs in solution exhibited a fast response to the outer magnetic field, and can be completely separated in several minutes. It was found that Ap-MNPs have good specificity to the target AFP, as the recovery of AFP (87.0%) was much higher than the competitive proteins IgG (38.9%), HSA (18.5%), and FIB (11.4%). A convenient and efficient label-free detection method of AFP in serum was developed based on Ap-MNPs in combination with high-performance liquid chromatography. The linearity of this method was over a range of 1-50 µg ml-1 with a correlation coefficient of 0.9999, and the limit of detection was 0.27 µg ml-1. This study indicated that aptamers are an ideal tool for the recognition and detection of biomarkers, and thus will find wide applications in clinical practice.


Subject(s)
Aptamers, Nucleotide/chemistry , Biosensing Techniques/methods , Carcinoma, Hepatocellular/blood , DNA, Single-Stranded/chemistry , Liver Neoplasms/blood , Magnetite Nanoparticles/chemistry , alpha-Fetoproteins/analysis , Aptamers, Nucleotide/blood , Biomarkers/blood , Biosensing Techniques/instrumentation , Humans , Nanotechnology/methods
7.
Anal Bioanal Chem ; 411(29): 7709-7716, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31300860

ABSTRACT

Early diagnosis of acute myocardial infarction (AMI) is of outmost importance to reduce the mortality rate, and cardiac troponins are considered the gold standard biomarkers of myocardial necrosis. In this scenario, the characterization of two troponin T (TnT)-binding aptamers as viable alternative to antibodies employed on clinical immunoassays is here reported for the first time. Their recognition ability was first investigated through surface plasmon resonance (SPR). Subsequently, an enzyme-linked oligonucleotide assay (ELONA) was developed on common 96-well polystyrene plates, both by direct and sandwich detection strategies for comparison. In both cases, the assay exhibits a detection ability of TnT in the range of low nanomolar but a great advantage on serum interference was obtained by using both aptamers in a sandwich format, with excellent reproducibility and recovery values. Despite the sensitivity needing to be enhanced to the low picomolar range, these results are encouraging for the development of new, low-cost, and rapid antibody-free colorimetric assays for AMI studies based on aptamer-Troponin T recognition.


Subject(s)
Aptamers, Nucleotide/blood , Enzyme-Linked Immunosorbent Assay/methods , Troponin T/blood , Biomarkers/blood , Colorimetry/methods , Early Diagnosis , Horseradish Peroxidase/metabolism , Humans , Myocardial Infarction/blood , Myocardial Infarction/diagnosis , Protein Binding , Reproducibility of Results , Surface Plasmon Resonance
8.
Small ; 15(19): e1900735, 2019 05.
Article in English | MEDLINE | ID: mdl-30963720

ABSTRACT

Emerging evidence indicates that exosomes derived from gastric cancer cells enhance tumor migration and invasion through the modulation of the tumor microenvironment. However, it remains a major problem to detect cancer-specific exosomes due to technical and biological challenges. Most of the methods reported could not achieve efficient detection of tumor-derived exosomes in the background of normal exosomes. Herein, a label-free electrochemical aptasensor is presented for specific detection of gastric cancer exosomes. This platform contains an anti-CD63 antibody modified gold electrode and a gastric cancer exosome specific aptamer. The aptamer is linked to a primer sequence that is complementary to a G-quadruplex circular template. The presence of target exosomes could trigger rolling circle amplification and produce multiple G-quadruplex units. This horseradish peroxidase mimicking DNAzyme could catalyze the reduction of H2 O2 and generate electrochemical signals. This aptasensor exhibits high selectivity and sensitivity toward gastric cancer exosomes with a detection limit of 9.54 × 102 mL-1 and a linear response range from 4.8 × 103 to 4.8 × 106 exosomes per milliliter. Therefore, this electrochemical aptasensor is expected to become a useful tool for the early diagnosis of gastric cancer.


Subject(s)
Aptamers, Nucleotide/chemistry , Electrochemical Techniques/methods , Exosomes/metabolism , G-Quadruplexes , Hemin/chemistry , Stomach Neoplasms/metabolism , Aptamers, Nucleotide/blood , Cell Line, Tumor , Early Detection of Cancer , Humans , Reproducibility of Results , Stomach Neoplasms/diagnosis
9.
J Med Chem ; 62(5): 2499-2507, 2019 03 14.
Article in English | MEDLINE | ID: mdl-30735377

ABSTRACT

RE31 is a 31-nt DNA aptamer, consisting of the G-quadruplex and a duplex domain, which is able to effectively prolong thrombin time. This article reports on the influence of certain modified nucleotide residues on thermodynamic and biological properties as well as the folding topology of RE31. Particularly, the effect of the presence of nucleosides in unlocked nucleic acid (UNA), locked nucleic acid (LNA), or ß-l-RNA series was evaluated. The studies presented herein show that all modified residues can influence thermal and biological stabilities of G-quadruplex in a position-dependent manner. The aptamers modified simultaneously with UNA at the T15 position and LNAs in the duplex part possess the highest value of melting temperature and a 2-fold higher anticoagulant effect. Importantly, RE31 variants modified with nucleosides in UNA, LNA, or ß-l-RNA series exhibit unchanged G-quadruplex folding topology. Crucially, introduction of any of the modified residues into RE31 causes prolongation of aptamer stability in human serum.


Subject(s)
Aptamers, Nucleotide/pharmacology , Nucleic Acid Conformation , Thermodynamics , Amides/metabolism , Aptamers, Nucleotide/blood , Aptamers, Nucleotide/chemistry , Blood Coagulation/drug effects , Drug Stability , Humans , Surface Plasmon Resonance , Thrombin/metabolism
10.
Talanta ; 194: 437-445, 2019 Mar 01.
Article in English | MEDLINE | ID: mdl-30609555

ABSTRACT

Ovarian cancer is regarded as the most lethal gynecologic malignancy with poor prognosis and high mortality rate. Drug-resistance was thought to be the main obstacle to improving overall survival rate of ovarian cancer. New ligands for drug-resistant ovarian cancer cells have potential for the development of diagnosis and therapy of ovarian cancer. In present work, we reported two aptamers, HF3-58 and HA5-68 generated by cell-SELEX, against a paclitaxel-resistant ovarian cancer cell line (A2780T). Both two aptamers exhibited high selectivity and strong affinity to target cells with low nanomolar dissociation constants. The binding of aptamers to target cells was independent of divalent ions, and was tolerant of incubation temperature and nucleases in serum. Molecular targets of the two aptamers were preliminarily demonstrated to be two different glycoproteins on cell surface of A2780T cells. Owing to the structure stability and high resistance to nuclease, these two aptamers had good performance in the detection of drug-resistant ovarian cancer cells in human serum.


Subject(s)
Aptamers, Nucleotide/metabolism , Drug Resistance, Neoplasm , Ovarian Neoplasms/pathology , SELEX Aptamer Technique , Aptamers, Nucleotide/blood , Aptamers, Nucleotide/genetics , Base Sequence , Cell Line, Tumor , Cell Membrane/metabolism , Female , Humans , Ovarian Neoplasms/metabolism
11.
ACS Chem Neurosci ; 10(3): 1706-1715, 2019 03 20.
Article in English | MEDLINE | ID: mdl-30605601

ABSTRACT

Specific analysis of such neurotransmitters as dopamine by the aptamer electrodes in biological fluids is detrimentally affected by nonspecific adsorption of media, particularly pronounced at positive charges of the electrode surface at which dopamine oxidizes. Here, we show that dopamine analysis at the RNA-aptamer/cysteamine-modified electrodes is strongly inhibited in undiluted human serum and blood due to nonspecific interfacial adsorption of serum and blood components. We demonstrate that nonspecific adsorption of serum proteins (but not of blood components) could be minimized when analysis is performed in a flow and injections of serum samples are followed by washing steps in a phosphate buffer solution (PBS) carrier. Under those conditions, the dopamine-aptamer binding affinity in whole human serum of (1.9 ± 0.3) × 104 M-1 s-1 was comparable to the (3.7 ± 0.3) × 104 M-1 s-1 found in PBS, and the dopamine oxidation signal linearly depended on the dopamine concentration, providing a sensitivity of analysis of 73 ± 3 nA µM-1 cm-2 and a LOD of 114 ± 8 nM. The flow-injection apatmer-electrode system was used for direct analysis of basal levels of dopamine in undiluted human serum samples, without using any physical separators (membranes) or filtration procedures. The results suggest a simple strategy for combatting biosurface fouling, otherwise most pronounced at positive electrode potentials used for dopamine detection, and assist in designing more efficient antifouling strategies for biomedical applications.


Subject(s)
Adsorption/physiology , Aptamers, Nucleotide/blood , Dopamine/blood , Electrodes , Biosensing Techniques/methods , Electrochemical Techniques/methods , Humans , Metal Nanoparticles/analysis , Oxidation-Reduction
12.
Biosens Bioelectron ; 123: 160-166, 2019 Jan 01.
Article in English | MEDLINE | ID: mdl-30139622

ABSTRACT

In this study, we report a cognate pair of the aptamer-based sandwich-type electrochemical biosensor for type 2 diabetes biomarker (Vaspin) using coccolith modified electrodeposited on the screen-printed gold electrode (CME-SPGE). The coccolith derived from E. huxleyi used in this study were known to be highly-structured microparticles with many nano-sized pores. The CME-SPGE was successfully fabricated by drop-casting coccoliths, followed by Au sputtering and electrodeposition of Au. On this CME-SPGE electrode, the sandwich-type electrochemical aptasensor was fabricated by using a cognate pair of aptamers. The morphological, electrochemical characteristics and the performances of both the CME-SPGE and the completely fabricated sandwich-type aptasensor were investigated by SEM, EDAX, cyclic voltammetry, and chronoamperometry. Due to the synergic effect of a cognate pair of aptamers on CME-SPGE, this newly developed sandwich-type electrochemical biosensor for Vaspin showed high specificity, and good sensitivity with a limit of detection (LOD) of 298 pM, along with more widen the linear range. To the best of our knowledge, this is the first report about the use of a coccolith modified electrode with a cognate pair aptamer resulting in sandwich-type binding in an electrochemical biosensor. With the advantages of using highly-structured biomineral microparticles and a cognate pair of aptamers, this new study may pave the innovative way to design a novel sandwich-type electrochemical aptasensor platform.


Subject(s)
Biomarkers/blood , Biosensing Techniques , Diabetes Mellitus, Type 2/blood , Serpins/isolation & purification , Aptamers, Nucleotide/blood , Aptamers, Nucleotide/genetics , Diabetes Mellitus, Type 2/pathology , Gold/chemistry , Humans , Metal Nanoparticles/chemistry , Serpins/blood
13.
J Pharm Biomed Anal ; 159: 341-347, 2018 Sep 10.
Article in English | MEDLINE | ID: mdl-30025299

ABSTRACT

The use of DNA aptamers in biosensors for the quantification of pharmaceuticals in the clinics would help to overcome the limitations of antibody-based detection for small molecules. The interest for such systems is proven by the ever-increasing number of aptamer-based solutions for analytics proposed in the literature as proof-of-concept demonstrators. Despite such diversity, these platforms often lack a comparative assessment of their performances against the current standard of practice in the clinics when using real samples. We employed an aptamer against tobramycin discovered in our laboratory to quantify through surface plasmon resonance the concentration of the antibiotic in clinical samples obtained from patients treated with tobramycin and undergoing therapeutic drug monitoring. We then compared the performances of our detection strategy against the current standard of practice. Our results show how, using adequate calibration and matrix complexity reduction, DNA aptamer-based direct assays can assess clinically relevant concentrations of small molecules in patient serum and with good correlation to current standards used in the clinics.


Subject(s)
Aptamers, Nucleotide/blood , Drug Monitoring/standards , Tobramycin/blood , Anti-Bacterial Agents/blood , Drug Monitoring/methods , Humans , Surface Plasmon Resonance
14.
Lab Chip ; 18(4): 574-584, 2018 02 13.
Article in English | MEDLINE | ID: mdl-29299579

ABSTRACT

To perform precision medicine in real-time, a sensor capable of continuously monitoring target biomolecules secreted from a patient under dynamic situations is essential. In this study, a novel portable device combining an aptamer probe and a nanofluidic component was developed, enabling the buffer-free continuous monitoring of small molecules in biological fluids. This integration is synergistic: the aptamer sensor is used to bind target biomolecules, triggering a fluorescence signal change, while the nanofluidic component is applied to achieve ion concentration polarization and convert serum into a clean buffer for aptamer signal regeneration. To demonstrate the system's versatility, we measured various adenosine triphosphate concentrations in human serum for hours with high sensitivity and specificity at minute temporal resolution. Our results demonstrate that this integrative device can be applied for the continuous measurement of target biomolecules and online signal regeneration in patient samples without the use of bulky clean buffer solutions for dynamic real-time healthcare.


Subject(s)
Adenosine Triphosphate/blood , Aptamers, Nucleotide/blood , Biosensing Techniques , Body Fluids/chemistry , Microfluidic Analytical Techniques , Nanotechnology , Fluorescence , Humans , Ions/blood , Time Factors
15.
Nanotechnology ; 29(9): 095602, 2018 Mar 02.
Article in English | MEDLINE | ID: mdl-29271356

ABSTRACT

Due to its predictable self-assembly and structural stability, structural DNA nanotechnology is considered one of the main interdisciplinary subjects encompassing conventional nanotechnology and biotechnology. Here we have fabricated the mucin aptamer (MUC1)-conjugated DNA nano-ring intercalated with doxorubicin (DNRA-DOX) as potential therapeutics for breast cancer. DNRA-DOX exhibited significantly higher cytotoxicity to the MCF-7 breast cancer cells than the controls, including DOX alone and the aptamer deficient DNA nano-ring (DNR) with doxorubicin. Interactions between DOX and DNRA were studied using spectrophotometric measurements. Dose-dependent cytotoxicity was performed to prove that both DNR and DNRA were non-toxic to the cells. The drug release profile showed a controlled release of DOX at normal physiological pH 7.4, with approximately 61% released, but when exposed to lysosomal of pH 5.5, the corresponding 95% was released within 48 h. Owing to the presence of the aptamer, DNRA-DOX was effectively taken up by the cancer cells, as confirmed by confocal microscopy, implying that it has potential for use in targeted drug delivery.


Subject(s)
Aptamers, Nucleotide/blood , DNA/chemistry , Drug Carriers/chemistry , Nanoparticles/chemistry , Cell Proliferation/drug effects , Doxorubicin/pharmacology , Humans , MCF-7 Cells , Mucins/chemistry
16.
Nucleic Acid Ther ; 27(6): 335-344, 2017 Dec.
Article in English | MEDLINE | ID: mdl-28945147

ABSTRACT

There is increasing interest in the use of aptamers for the development of therapeutics. However, as oligonucleotides, aptamers are susceptible to nuclease degradation; poor serum stability is likely to negatively affect in vivo function. Modified nucleotides have been used to thwart nuclease degradation. However, few studies report the serum stability of selected aptamers. In this study, we examined the effect of various chemical modifications (2'-deoxy, 2'-hydroxyl, 2'-fluoro, and 2'-O-methyl) on the stability of a control oligonucleotide sequence following incubation in frozen human, fresh mouse, and fresh human serum. We also assessed the effect of the 3' inverted dT cap on stability. Surprisingly, we found that fYrR (2'-fluoro RNA) is only roughly as stable as DNA (2'-deoxy). Interestingly, the inclusion of a 3' inverted dT cap had only a modest effect on serum stability, if any. In one instance, the addition of a 3' inverted dT cap rendered a molecule composed of DNA more stable than its fYrR counterpart. By far, fully modified oligonucleotides (100% 2-O-Methyl or 2'-O-methyl A, C, and U in combination with 2'-fluoro G, termed fGmH) had the longest half-lives. These compositions demonstrated little degradation in human serum even after prolonged incubation. Together these results support the need for using fully modified aptamers for in vivo applications and should encourage those in the field to exploit newer polymerase variants capable of directly generating such polymers.


Subject(s)
Aptamers, Nucleotide/blood , Aptamers, Nucleotide/chemistry , RNA/blood , Serum/chemistry , Animals , Aptamers, Nucleotide/chemical synthesis , Base Sequence , DNA/blood , DNA/chemistry , Drug Discovery , Female , Half-Life , Humans , Mice , Mice, Inbred C57BL , RNA/chemistry , RNA Stability
17.
Nucleic Acid Ther ; 27(6): 345-353, 2017 Dec.
Article in English | MEDLINE | ID: mdl-28961063

ABSTRACT

The addition of novel side chains at the 5-position of uracil is an effective means to increase chemical diversity of aptamers and hence the success rate for discovery of high-affinity ligands to protein targets. Such modifications also increase nuclease resistance, which is useful in a range of applications, especially for therapeutics. In this study, we assess the impact of these side chains on plasma pharmacokinetics of modified aptamers conjugated to a 40 kDa polyethylene glycol. We show that clearance from plasma depends on relative hydrophobicity: side chains with a negative cLogP (more hydrophilic) result in slower plasma clearance compared with side chains with a positive cLogP (more hydrophobic). We show that clearance increases with the number of side chains in sequences of ≥28 synthons, but this effect is dramatically diminished in shorter sequences. These results serve as a guide for the design of new therapeutic aptamers with diversity-enhancing side chains.


Subject(s)
Aptamers, Nucleotide/chemistry , Aptamers, Nucleotide/pharmacokinetics , Polyethylene Glycols/chemistry , Uracil/chemistry , Animals , Aptamers, Nucleotide/administration & dosage , Aptamers, Nucleotide/blood , Base Sequence , Drug Design , Hydrophobic and Hydrophilic Interactions , Ligands , Linear Models , Male , Polyethylene Glycols/metabolism , Rats , Rats, Sprague-Dawley , SELEX Aptamer Technique/methods , Statistics, Nonparametric , Uracil/metabolism
18.
Tumour Biol ; 39(7): 1010428317717123, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28718373

ABSTRACT

Lung cancer is by far the leading cause of cancer death in the world. Despite the improvements in diagnostic methods, the status of early detection was not achieved. So, a new diagnostic method is needed. The aim of this study is to obtain the highly specific nucleic acid aptamers with strong affinity to tumor markers in the serum of the lung cancer patients for targeting the serum. Aptamers specifically binding to tumor markers in the serum of the lung cancer patients were screened from the random single-stranded DNA library with agarose beads as supports and the serum as a target by target-substituting subtractive SELEX technique and real-time quantitative polymerase chain reaction technique. Subsequently, the secondary single-stranded DNA library obtained by 10 rounds of screening was amplified to double-stranded DNA, followed by high-throughput genome sequence analysis to screen aptamers with specific affinity to tumor markers in the serum of the lung cancer patients. Finally, six aptamers obtained by 10 rounds of screening were identified with high specific affinity to tumor markers in the serum of the lung cancer patients. Compared with other five aptamers, the aptamer 43 was identified both with the highest specificity to bind target molecule and without any obvious affinity to non-specific proteins. The screened aptamers have relatively high specificity to combine tumor markers in the serum of the lung cancer patients, which provides breakthrough points for early diagnosis and treatment of lung cancer.


Subject(s)
Aptamers, Nucleotide/blood , Biomarkers, Tumor/blood , Early Diagnosis , Lung Neoplasms/blood , Aptamers, Nucleotide/genetics , Biomarkers, Tumor/genetics , DNA, Single-Stranded/blood , Female , Gene Library , Humans , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Male , Protein Binding , SELEX Aptamer Technique
19.
Biomed Pharmacother ; 93: 931-938, 2017 Sep.
Article in English | MEDLINE | ID: mdl-28715874

ABSTRACT

Nuclear medicine clinicians are still waiting for the optimal scintigraphic imaging agents capable of distinguishing between infection and inflammation, and between fungal and bacterial infections. Aptamers have several properties that make them suitable for molecular imaging. In the present study, a peptidoglycan aptamer (Antibac1) was labeled with 99mTc and evaluated by biodistribution studies and scintigraphic imaging in infection-bearing mice. Labeling with 99mTc was performed by the direct method and the complex stability was evaluated in saline, plasma and in the molar excess of cysteine. The biodistribution and scintigraphic imaging studies with the 99mTc-Antibac1 were carried out in two different experimental infection models: Bacterial-infected mice (S. aureus) and fungal-infected mice (C. albicans). A 99mTc radiolabeled library, consisting of oligonucleotides with random sequences, was used as a control for both models. Radiolabeling yields were superior to 90% and 99mTc-Antibac1 was highly stable in presence of saline, plasma, and cysteine up to 6h. Scintigraphic images of S. aureus infected mice at 1.5 and 3.0h after 99mTc-Antibac1 injection showed target to non-target ratios of 4.7±0.9 and 4.6±0.1, respectively. These values were statistically higher than those achieved for the 99mTc-library at the same time frames (1.6±0.4 and 1.7±0.4, respectively). Noteworthy, 99mTc-Antibac1 and 99mTc-library showed similar low target to non-target ratios in the fungal-infected model: 2.0±0.3 and 2.0±0.6for 99mTc-Antibac1 and 2.1±0.3 and 1.9 ± 0.6 for 99mTc-library, at the same times. These findings suggest that the 99mTc-Antibac1 is a feasible imaging probe to identify a bacterial infection focus. In addition, this radiolabeled aptamer seems to be suitable in distinguishing between bacterial and fungal infection.


Subject(s)
Aptamers, Nucleotide/blood , Bacterial Infections/blood , Bacterial Infections/diagnostic imaging , Peptidoglycan/blood , Technetium/blood , Animals , Candida albicans/isolation & purification , Mice , Radionuclide Imaging/methods , Staphylococcus aureus/isolation & purification
20.
Molecules ; 22(6)2017 Jun 08.
Article in English | MEDLINE | ID: mdl-28594360

ABSTRACT

Nucleic acid ligands, aptamers, harbor the unique characteristics of small molecules and antibodies. The specificity and high affinity of aptamers enable their binding to different targets, such as small molecules, proteins, or cells. Chemical modifications of aptamers allow increased bioavailability. A further great benefit of aptamers is the antidote (AD)-mediated controllability of their effect. In this study, the AD-mediated complexation and neutralization of the thrombin binding aptamer NU172 and Toll-like receptor 9 (TLR9) binding R10-60 aptamer were determined. Thereby, the required time for the generation of aptamer/AD-complexes was analyzed at 37 °C in human serum using gel electrophoresis. Afterwards, the blocking of aptamers' effects was analyzed by determining the activated clotting time (ACT) in the case of the NU172 aptamer, or the expression of immune activation related genes IFN-1ß, IL-6, CXCL-10, and IL-1ß in the case of the R10-60 aptamer. Gel electrophoresis analyses demonstrated the rapid complexation of the NU172 and R10-60 aptamers by complementary AD binding after just 2 min of incubation in human serum. A rapid neutralization of anticoagulant activity of NU172 was also demonstrated in fresh human whole blood 5 min after addition of AD. Furthermore, the TLR9-mediated activation of PMDC05 cells was interrupted after the addition of the R10-60 AD. Using these two different aptamers, the rapid antagonizability of the aptamers was demonstrated in different environments; whole blood containing numerous proteins, cells, and different small molecules, serum, or cell culture media. Thus, nucleic acid ADs are promising molecules, which offer several possibilities for different in vivo applications, such as antagonizing aptamer-based drugs, immobilization, or delivery of oligonucleotides to defined locations.


Subject(s)
Aptamers, Nucleotide/blood , Toll-Like Receptor 9/blood , Anticoagulants/blood , Anticoagulants/chemistry , Antidotes/chemistry , Aptamers, Nucleotide/chemistry , Blood Coagulation/genetics , Humans , Ligands , SELEX Aptamer Technique , Thrombin/chemistry , Thrombin/genetics , Toll-Like Receptor 9/chemistry
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