Rational Truncation of an RNA Aptamer to Prostate-Specific Membrane Antigen Using Computational Structural Modeling

No abstract is available for this paper.

• Publication year

  2011

• Venue

  Nucleic Acid Therapeutics

• Publication date

  2011-10-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1089/nat.2011.0313PMID 22004414PMCID PMC3198747
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Structural Bioinformatics

  2021influential reference
• An Aptamer-siRNA Chimera Suppresses HIV-1 Viral Loads and Protects from Helper CD4+ T Cell Decline in Humanized Mice

  2011cited by this paper
• Affinity hydrogels for controlled protein release using nucleic acid aptamers and complementary oligonucleotides.

  2011cited by this paper
• Targeted delivery of a cisplatin prodrug for safer and more effective prostate cancer therapy in vivo

  2011cited by this paper
• Structural prediction and binding analysis of hybridized aptamers

  2011cited by this paper
• Physics-based de novo prediction of RNA 3D structures.

  2011cited by this paper
• Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay

  2010cited by this paper
• AS-1411, a guanosine-rich oligonucleotide aptamer targeting nucleolin for the potential treatment of cancer, including acute myeloid leukemia.

  2010cited by this paper
• Expression of prostate‐specific membrane antigen (PSMA), increases cell folate uptake and proliferation and suggests a novel role for PSMA in the uptake of the non‐polyglutamated folate, folic acid

  2010influential reference
• MDockPP: A hierarchical approach for protein‐protein docking and its application to CAPRI rounds 15–19

  2010cited by this paper
• Aptamers as therapeutics

  2010cited by this paper
• Folding kinetics for the conformational switch between alternative RNA structures.

  2010cited by this paper
• Coagulation Factor IXa as a Target for Treatment and Prophylaxis of Venous Thromboembolism

  2010cited by this paper
• Reversible cell-specific drug delivery with aptamer-functionalized liposomes.

  2009cited by this paper
• Therapeutic Applications of DNA and RNA Aptamers

  2009cited by this paper
• The prostate specific membrane antigen regulates the expression of IL-6 and CCL-5 in prostate tumour cells by activating the MAPK pathways

  2009cited by this paper
• Targeted delivery of cisplatin to prostate cancer cells by aptamer functionalized Pt(IV) prodrug-PLGA–PEG nanoparticles

  2009cited by this paper
• Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors

  2009influential reference
• Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells

  2009cited by this paper
• Prostate-specific membrane antigen targeted imaging and therapy of prostate cancer using a PSMA inhibitor as a homing ligand.

  2009cited by this paper
• Dependence of aptamer activity on opposed terminal extensions: improvement of light-regulation efficiency

  2009cited by this paper
• A new computational approach for mechanical folding kinetics of RNA hairpins.

  2009cited by this paper
• ARC-1779, a PEGylated aptamer antagonist of von Willebrand factor for potential use as an anticoagulant or antithrombotic agent.

  2009cited by this paper
• Aptamers as a model for functional evaluation of LNA and 2'-amino LNA.

  2009cited by this paper
• The Prostate Specific Membrane Antigen Regulates the Expression of IL-6 and CCL5 in Prostate Tumour Cells by Activating the MAPK Pathways1

  2009cited by this paper
• Characterizing ribonucleases in vitro examples of synergies between biochemical and structural analysis.

  2008cited by this paper
• An iterative knowledge‐based scoring function for protein–protein recognition

  2008cited by this paper
• Multivalent 4-1BB binding aptamers costimulate CD8+ T cells and inhibit tumor growth in mice.

  2008cited by this paper
• RNA folding: conformational statistics, folding kinetics, and ion electrostatics.

  2008cited by this paper
• Post-SELEX chemical optimization of a trypanosome-specific RNA aptamer.

  2008cited by this paper
• Novel dual inhibitory function aptamer-siRNA delivery system for HIV-1 therapy.

  2008cited by this paper
• Targeted delivery of cisplatin to prostate cancer cells by aptamer functionalized Pt(IV) prodrug-PLGA–PEG nanoparticles

  2008influential reference
• Precise engineering of targeted nanoparticles by using self-assembled biointegrated block copolymers

  2008cited by this paper
• Exploring the sequence space of a DNA aptamer using microarrays

  2007cited by this paper
• First-inHuman Evaluation of Anti – von Willebrand Factor Therapeutic Aptamer ARC 1779 in Healthy Volunteers

  2007cited by this paper
• First-in-Human Evaluation of Anti–von Willebrand Factor Therapeutic Aptamer ARC1779 in Healthy Volunteers

  2007cited by this paper
• RNA Secondary Structure Prediction

  2007cited by this paper
• An aptamer-doxorubicin physical conjugate as a novel targeted drug-delivery platform.

  2006cited by this paper
• Year 2 efficacy results of 2 randomized controlled clinical trials of pegaptanib for neovascular age-related macular degeneration.

  2006cited by this paper
• Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes.

  2006cited by this paper
• Tumor targeting by an aptamer.

  2006cited by this paper
• Anti‐VEGF Aptamer (Pegaptanib) Therapy for Ocular Vascular Diseases

  2006cited by this paper
• Aptamer mediated siRNA delivery

  2006cited by this paper
• RNA Secondary Structure Analysis Using RNAstructure

  2006influential reference
• 2´-Deoxy Purine, 2´-O-Methyl Pyrimidine (dRmY) Aptamers as Candidate Therapeutics

  2006cited by this paper
• First-in-Human Experience of an Antidote-Controlled Anticoagulant Using RNA Aptamer Technology: A Phase 1a Pharmacodynamic Evaluation of a Drug-Antidote Pair for the Controlled Regulation of Factor IXa Activity

  2006cited by this paper
• Cell type–specific delivery of siRNAs with aptamer-siRNA chimeras

  2006influential reference
• The Amber biomolecular simulation programs

  2005cited by this paper
• Crystal structure of prostate-specific membrane antigen, a tumor marker and peptidase

  2005cited by this paper
• Direct in vitro selection of a 2'-O-methyl aptamer to VEGF.

  2005cited by this paper
• Oligo- and poly-nucleotides: 50 years of chemical synthesis.

  2005cited by this paper
• Predicting RNA folding thermodynamics with a reduced chain representation model.

  2005cited by this paper
• Pharmacokinetics and Biodistribution of Novel Aptamer Compositions

  2004cited by this paper
• Nanoparticle-Aptamer Bioconjugates

  2004cited by this paper
• Pegaptanib for neovascular age-related macular degeneration.

  2004cited by this paper
• Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen.

  2002influential reference
• RNA aptamers as reversible antagonists of coagulation factor IXa

  2002cited by this paper
• Cloning, expression, genomic localization, and enzymatic activities of the mouse homolog of prostate-specific membrane antigen/NAALADase/folate hydrolase

  2001cited by this paper
• Prostate‐specific membrane antigen (PSMA) enzyme activity is elevated in prostate cancer cells

  2000influential reference
• Generation of a baculovirus recombinant prostate-specific membrane antigen and its use in the development of a novel protein biochip quantitative immunoassay.

  2000cited by this paper
• Anti-L-Selectin Aptamers: Binding Characteristics, Pharmacokinetic Parameters, and Activity Against an Intravascular Target In Vivo

  2000cited by this paper
• Efficient synthesis of nucleic acids heavily modified with non-canonical ribose 2'-groups using a mutantT7 RNA polymerase (RNAP).

  1999cited by this paper
• Novel approach to specific growth factor inhibition in vivo: antagonism of platelet-derived growth factor in glomerulonephritis by aptamers.

  1999cited by this paper
• Derivation of RNA aptamer inhibitors of human complement C5.

  1999cited by this paper
• 2′-Fluoropyrimidine RNA-based Aptamers to the 165-Amino Acid Form of Vascular Endothelial Growth Factor (VEGF165)

  1998cited by this paper
• Prostate-specific membrane antigen expression in normal and malignant human tissues.

  1997cited by this paper
• Mechanism of ribose 2'-group discrimination by an RNA polymerase.

  1997cited by this paper
• Comprehensive chemical modification interference and nucleotide substitution analysis of an RNA pseudoknot inhibitor to HIV-1 reverse transcriptase.

  1995cited by this paper
• Potent 2'-amino-2'-deoxypyrimidine RNA inhibitors of basic fibroblast growth factor.

  1995cited by this paper
• Stability, specific binding activity, and plasma concentration in mice of an oligodeoxynucleotide modified at 5'-terminal with poly(ethylene glycol).

  1995cited by this paper
• Structural probing and damage selection of citrulline- and arginine-specific RNA aptamers identify base positions required for binding.

  1995cited by this paper
• Predicting thermodynamic properties of RNA.

  1995cited by this paper
• Modified RNA sequence pools for in vitro selection.

  1994cited by this paper
• A double-filter method for nitrocellulose-filter binding: application to protein-nucleic acid interactions.

  1993cited by this paper
• An RNA motif that binds ATP

  1993cited by this paper
• In vitro selection of RNA molecules that bind specific ligands

  1990cited by this paper

• Molecular dynamics analysis of HbA1c-binding aptamer selectivity and stability for aptasensor development

  2026influential citation
• Conjugation of hydrophobic drugs to motile pRNA 4WJ nanoparticles for spontaneous tumor targeting and undetectable toxicity.

  2026cites this paper
• Molecular bioengineering of functional nucleic acids

  2025cites this paper
• Nanotechnology Meets the Tumor Microenvironment: Unlocking New Horizons in Cancer Therapy.

  2025cites this paper
• Aptamer-CRISPR/Cas12a-Based Lateral Flow Technique for Visualized Rapid Detection of Endogenous Damage Factor Neu5Gc in Red Meat

  2025cites this paper
• Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives.

  2025cites this paper
• RNA Nanoparticles Harboring Radioisotopes or Other Imaging Molecules for Spontaneous Tumor Targeting for Early Cancer Diagnosis

  2025cites this paper
• Nucleic acid aptamers in orthopedic diseases: promising therapeutic agents for bone disorders

  2025cites this paper
• Advanced strategies for screening and identifying RNA-targeted small molecules: Bridging therapeutic potential and innovation

  2025cites this paper
• Using aptamers for targeted delivery of RNA therapies

  2025cites this paper
• Nano‐Phase Separation and Analyte Binding in Aptasensors Investigated by Nano‐IR Spectroscopy

  2025cites this paper
• A Truncated Multi-Thiol Aptamer-Based SARS-CoV-2 Electrochemical Biosensor: Towards Variant-Specific Point-of-Care Detection with Optimized Fabrication

  2025cites this paper
• Harnessing in Silico Design for Electrochemical Aptasensor Optimization: Detection of Okadaic Acid (OA)

  2025cites this paper
• A highly sensitive SERS aptasensor using a novel truncated aptamer for the detection of Deoxynivalenol

  2024cites this paper
• A comprehensive investigation of the biophysical approach for aptamer functionalized nanoparticles in cancer therapy: a review

  2024cites this paper
• In silico selection of aptamers against SARS-CoV-2.

  2024cites this paper
• Targeted Delivery of Potent Chemical Drugs and RNAi to Drug-Resistant Breast Cancer Using RNA-Nanotechnology and RNA-Ligand Displaying Extracellular vesicles

  2024cites this paper
• Prediction of aptamer affinity using an artificial intelligence approach.

  2024cites this paper
• The neutralisation and inhibitory effects of new tRNA-mimetic aptamer against cytotoxin-induced cytotoxicity in human skin keratinocytes

  2024cites this paper
• Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications.

  2024cites this paper
• Prostate-Specific Membrane Antigen-Targeted NIR Phototheranostics for Prostate Cancer.

  2024cites this paper
• Specific Delivery of MiRNA for High Efficient Inhibition of Prostate Cancer by RNA Nanotechnology.

  2024cites this paper
• Generation of an RNA aptamer against LipL32 of Leptospira isolated by Tripartite-hybrid SELEX coupled with in-house Python-aided unbiased data sorting.

  2023cites this paper
• RNA aptamer-mediated gene therapy of prostate cancer: lessons from the past and future directions

  2023influential citation
• Smart nanoparticles for cancer therapy

  2023cites this paper
• The Diagnostic Potential of RNA Aptamers against the NS1 Protein of Dengue Virus Serotype 2

  2023cites this paper
• ΔPSap4#5 surface-functionalized abiraterone-loaded nanoparticle successfully inhibits carcinogen-induced prostate cancer in mice: a mechanistic investigation

  2023cites this paper
• Synthesis of Isolated DNA Aptamer and Its Application of AC-Electrothermal Flow-Based Rapid Biosensor for the Detection of Dengue Virus in a Spiked Sample.

  2023cites this paper
• Design and Prediction of Aptamers Assisted by In Silico Methods

  2023influential citation
• Structural properties and binding mechanism of DNA aptamers sensing saliva melatonin for diagnosis and monitoring of circadian clock and sleep disorders.

  2023cites this paper
• The Aptamer Functionalized Nanocomposite Used for Prostate Cancer Diagnosis and Therapy

  2022cites this paper
• Identification of novel aptamers targeting cathepsin B-overexpressing prostate cancer cells

  2022cites this paper
• Optimization of Short RNA Aptamers for TNBC Cell Targeting

  2022cites this paper
• Development of a Molecular Aptamer Beacon Applied to Magnetic-Assisted RNA Extraction for Detection of Dengue and Zika Viruses Using Clinical Samples

  2022cites this paper
• Targeted delivery of RNAi to cancer cells using RNA-ligand displaying exosome

  2022cites this paper
• Selection and characterization of bispecific aptamers against malachite green and leucomalachite green.

  2022cites this paper
• Optimization of an aptamer against Prorocentrum minimum - A common harmful algae by truncation and G-quadruplex-forming mutation.

  2022cites this paper
• Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines?

  2022cites this paper
• Targeting signaling pathways in prostate cancer: mechanisms and clinical trials

  2022cites this paper
• Metamorphosis of prostate specific membrane antigen (PSMA) inhibitors

  2022cites this paper
• Recent progress in the development of aptasensors for cancer diagnosis: Focusing on aptamers against cancer biomarkers

  2021cites this paper
• Characterization of DNA aptamer-protein binding using fluorescence anisotropy assays in low-volume, high-efficiency plates.

  2021cites this paper
• Artificial Intelligence in Aptamer–Target Binding Prediction

  2021cites this paper
• Determination of minimal sequence for zearalenone aptamer by computational docking and application on an indirect competitive electrochemical aptasensor

  2021cites this paper
• Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.

  2021cites this paper
• Advances in PSMA-targeted therapy for prostate cancer

  2021cites this paper
• De novo ssRNA Aptamers against the SARS-CoV-2 Main Protease: In Silico Design and Molecular Dynamics Simulation

  2021cites this paper
• A comparative analysis of cell surface targeting aptamers

  2021cites this paper
• Methods and Applications of In Silico Aptamer Design and Modeling

  2020cites this paper
• Aptamer‐Incorporated Nanoparticle Systems for Drug Delivery

  2020cites this paper
• Aptamer-conjugated PLGA nanoparticles for delivery and imaging of cancer therapeutic drugs.

  2020cites this paper
• Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer

  2020cites this paper
• Scoring functions for protein-RNA complex structure prediction: advances, applications, and future directions

  2020cites this paper
• Strategies to bioengineer aptamer-driven nanovehicles as exceptional molecular tools for targeted therapeutics: A review.

  2020cites this paper
• Metal-labeled Aptamers as Novel nanoprobes for Imaging Mass Cytometry Analysis.

  2020cites this paper
• Aptamer-conjugated mesoporous silica nanoparticles for simultaneous imaging and therapy of cancer

  2020cites this paper
• Improved Cancer Targeting by Multimerizing Aptamers on Nanoscaffolds

  2020cites this paper
• Sensitive diagnosis of alpha-fetoprotein by a label free nanoaptasensor designed by modified Au electrode with spindle-shaped gold nanostructure

  2019cites this paper
• Fluorometric determination of lipopolysaccharides via changes of the graphene oxide-enhanced fluorescence polarization caused by truncated aptamers

  2019cites this paper
• Developing slow-off dickkopf-1 aptamers for early-diagnosis of hepatocellular carcinoma.

  2019cites this paper
• Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS

  2019cites this paper
• Aptamers in drug design: An emerging weapon to fight a losing battle.

  2019cites this paper
• Characterization of A Bifunctional Synthetic RNA Aptamer and A Truncated Form for Ability to Inhibit Growth of Non-Small Cell Lung Cancer

  2019cites this paper
• Targeted siRNA delivery using aptamer-siRNA chimeras and aptamer-conjugated nanoparticles.

  2018cites this paper
• Therapeutic aptamers in discovery, preclinical and clinical stages

  2018cites this paper
• Competition-Enhanced Ligand Selection to Identify DNA Aptamers.

  2018cites this paper
• Aptamer as Therapeutics for Cancer with Focus on Retinoblastoma

  2018cites this paper
• Detection and treatment of critical illnesses using oligonucleotides

  2018influential citation
• Aptamer-conjugated multi-walled carbon nanotubes as a new targeted ultrasound contrast agent for the diagnosis of prostate cancer

  2018cites this paper
• Engineering of Supramolecular RNA Structures

  2018cites this paper
• Prediction of shorter oligonucleotide sequences recognizing aflatoxin M1

  2018cites this paper
• An electrochemical dopamine aptasensor using the modified Au electrode with spindle-shaped gold nanostructure

  2018cites this paper
• Selection and Identification of Skeletal-Muscle-Targeted RNA Aptamers

  2018cites this paper
• Thermodynamic and first-principles biomolecular simulations applied to synthetic biology: promoter and aptamer designs

  2018cites this paper
• Aptamers and apple pies: a mini-review of PSMA aptamers and lessons from Donald S. Coffey.

  2018cites this paper
• Bioinformatics Algorithms for Molecular Docking: IT and Chemistry Synergy

  2018cites this paper
• Favorable biodistribution, specific targeting and conditional endosomal escape of RNA nanoparticles in cancer therapy.

  2018cites this paper
• Stepping Library-Based Post-SELEX Strategy Approaching to the Minimized Aptamer in SPR.

  2017cites this paper
• In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target

  2017cites this paper
• Suppression of Prostate Cancer Metastasis by DPYSL3-Targeted saRNA.

  2017cites this paper
• Tumor cell-targeted delivery of CRISPR/Cas9 by aptamer-functionalized lipopolymer for therapeutic genome editing of VEGFA in osteosarcoma.

  2017cites this paper
• Advancement of the Emerging Field of RNA Nanotechnology

  2017cites this paper
• Discovery of Aptamer Ligands for Hepatic Stellate Cells Using SELEX

  2017cites this paper
• Nanoparticle Orientation to Control RNA Loading and Ligand Display on Extracellular Vesicles for Cancer Regression

  2017cites this paper
• Aptamer Cell-Based Selection: Overview and Advances

  2017cites this paper
• Chemical modification improves the stability of the DNA aptamer GBI-10 and its affinity towards tenascin-C.

  2017cites this paper
• Development of Diverse Size and Shape RNA Nanoparticles and Investigation of their Physicochemical Properties for Optimized Drug Delivery

  2017cites this paper
• Label-free fluorescence detection of melamine with a truncated aptamer.

  2016cites this paper
• Improved Synthesis and In Vitro Evaluation of an Aptamer Ribosomal Toxin Conjugate

  2016cites this paper
• lncRNA in the liver: Prospects for fundamental research and therapy by RNA interference.

  2016cites this paper
• Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes

  2016cites this paper
• In Silico Aptamer Docking Studies: From a Retrospective Validation to a Prospective Case Study'TIM3 Aptamers Binding.

  2016cites this paper
• Enhancing DPYSL3 gene expression via a promoter-targeted small activating RNA approach suppresses cancer cell motility and metastasis

  2016cites this paper
• Diagnosis of prostate cancer using anti-PSMA aptamer A10-3.2-oriented lipid nanobubbles

  2016influential citation
• Enhanced growth inhibition of prostate cancer in vitro and in vivo by a recombinant adenovirus-mediated dual-aptamer modified drug delivery system.

  2016cites this paper
• Method for Confirming Cytoplasmic Delivery of RNA Aptamers.

  2016cites this paper
• Specific Delivery of MiRNA for High Efficient Inhibition of Prostate Cancer by RNA Nanotechnology.

  2016cites this paper
• In vitro RNA SELEX for the generation of chemically-optimized therapeutic RNA drugs.

  2016influential citation
• Structural computational modeling of RNA aptamers.

  2016cites this paper
• In Silico Aptamer Docking Studies: From a Retrospective Validation to a Prospective Case Study-TIM3 Aptamers Binding.

  2016cites this paper