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Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

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Structural predictions of protein-DNA binding: MELD-DNA

Reza Esmaeeli et al.

Summary: MELD-DNA is a novel computational approach that predicts the structures of protein-DNA complexes and provides qualitative binding preferences between DNA sequences. It combines molecular dynamics simulations with Bayesian inference, incorporating general knowledge or experimental information. The method is sensitive to sequence-dependent properties and conformational changes required for binding, while information accelerates sampling of bound conformations.

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Targeted systematic evolution of an RNA platform neutralizing DNMT1 function and controlling DNA methylation

Carla L. Esposito et al.

Summary: DNA methylation is a crucial mechanism for regulating gene expression, and its aberration is commonly observed in cancer cells. This study developed a novel RNA-based approach, aptaDiR, which combines the inhibitory function of RNA with an aptamer platform to specifically target DNMT1. Through molecular modelling and experimental validation, aptaDiR was shown to effectively block DNA methylation, inhibit cancer cell viability, and suppress tumor growth in vivo. This innovative RNA strategy provides an alternative to the non-specific hypomethylating protocols currently approved, offering significant potential for improving clinical interventions on DNA methylation.

NATURE COMMUNICATIONS (2023)

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Review Biophysics

Prospects and Limitations of High-Resolution Single-Particle Cryo-Electron Microscopy

Ashwin Chari et al.

Summary: Single particle cryo-electron microscopy (cryo-EM) has become a robust method for determining biological macromolecule structures. Continuous improvements in hardware and software have contributed to an increasing number of solved structures. This review discusses the steps in developing and challenges of cryo-EM methodology, as well as potential future developments.

ANNUAL REVIEW OF BIOPHYSICS (2023)

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Review Biochemistry & Molecular Biology

Targeting Protein-Protein Interfaces with Peptides: The Contribution of Chemical Combinatorial Peptide Library Approaches

Alessandra Monti et al.

Summary: Protein-protein interfaces play crucial roles in pathophysiological pathways and are important targets for therapeutic compounds. However, identifying binding sites on protein surfaces and developing modulators of protein-protein interactions remain challenging due to their dynamic nature. Various strategies, including structural, computational, and combinatorial approaches, have been developed to characterize PPIs. Peptides are particularly potent and selective for inhibiting PPIs. This review discusses the impact of chemical peptide libraries in medicinal chemistry, focusing on recent applications, and explores the role of this methodology in the era of predictive approaches based on artificial intelligence in structural biology.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

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Article Biochemistry & Molecular Biology

Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection

Md Shafiqur Rahman et al.

Summary: This study reports the development of aptamers that effectively interfere with SARS-CoV-2 infection by targeting its spike protein, which plays a crucial role in the virus' entry into host cells. The researchers determined the three-dimensional structures of aptamer/receptor-binding domain complexes and developed bivalent aptamers that target different regions of the spike protein. By optimizing these aptamers, a bivalent aptamer with a stronger inhibitory effect on virus infection was created. This study highlights the potential of structure-based aptamer design for developing antiviral drugs against SARS-CoV-2 and other viruses.

MOLECULES (2023)

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Article Biochemistry & Molecular Biology

Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand

Adrien Chauvier et al.

Summary: This study investigates the interaction between RNA polymerase and nascent transcripts during transcription. It is found that the transcription process of a preQ(1) riboswitch can be modulated by the RNA polymerase and the conformation of the nascent RNA. Ligand binding to the riboswitch leads to the release of RNA polymerase pause and the continuation of transcription. The mechanism by which riboswitch folding modulates pausing is revealed through cryo-electron microscopy reconstructions.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2023)

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News Item Biotechnology & Applied Microbiology

FDA approves second RNA aptamer

Asher Mullard

NATURE REVIEWS DRUG DISCOVERY (2023)

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Article Biochemistry & Molecular Biology

Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide

Romualdo Troisi et al.

Summary: This study characterizes the interaction between a highly dynamic G-rich oligonucleotide, M08s-1, and its target protein, human α-thrombin. The study reveals that the anticoagulant activity of M08s-1 is mainly due to its adoption of a kinked structural organization formed by a G-quadruplex domain and a long duplex module. This unique structural feature hinders the approach of a protein substrate to the active site region, leading to an increase in the anticoagulant activity.

NUCLEIC ACIDS RESEARCH (2023)

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Review Biochemistry & Molecular Biology

When will RNA get its AlphaFold moment?

Bohdan Schneider et al.

Summary: Due to limited data and quality issues, it is challenging to predict the 3D structure of RNA using deep learning methods like AlphaFold in the short term. However, by addressing data quality and volume issues, utilizing more data, and developing new machine learning methods, an accurate RNA structure prediction method can be created.

NUCLEIC ACIDS RESEARCH (2023)

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Article Multidisciplinary Sciences

The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction

Bejo Ropii et al.

Summary: This study generated three-dimensional models of RNA aptamers using computational methods and compared them with experimentally determined structures. The results showed that the combination of mFold, RNAComposer, and molecular dynamics simulation could produce RNA aptamers with similar structures to the experimental results. This method has the potential to enhance the efficiency of RNA aptamer research and applications.

PLOS ONE (2023)

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Review Chemistry, Multidisciplinary

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Cailing Ji et al.

Summary: Aptamers, single-stranded oligonucleotides generated by in vitro evolution, have the ability to interact specifically with proteins. Modulating the structure of aptamers can significantly affect their protein interactions and related cellular behaviors. Analytical assays based on aptamer-protein interactions have been widely developed as a powerful tool for biomolecular detection. This review comprehensively introduces methods for regulating aptamer-protein interactions, elaborates on detection techniques for analyzing such interactions, and summarizes the analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules.

CHEMICAL REVIEWS (2023)

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Review Hematology

New insight into the traditional model of the coagulation cascade and its regulation: illustrated review of a three-dimensional view

Romuald Troisi et al.

Summary: The coagulation process relies on complex three-dimensional structural interactions and subtle biological regulations. Recent investigations have provided structural information on all players involved in the process, including single factors and multidomain proteins. Cryogenic electron microscopy techniques have revealed the structural features of highly complex coagulation factors. This review focuses on the structure of individual factors and their roles in intrinsic, extrinsic, and common pathways, providing clues on the structural recognition of factors involved in functional partnerships. The review also describes recent structures of important complexes formed by these proteins, with a focus on anticoagulant drugs and their reversal agents. Finally, the review highlights the potential roles of innovative biomolecules, such as aptamers, in regulating the cascade.

RESEARCH AND PRACTICE IN THROMBOSIS AND HAEMOSTASIS (2023)

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Article Cardiac & Cardiovascular Systems

Diagnostic and Therapeutic Aptamers

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JACC-Basic to Translational Science (2023)

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Review Chemistry, Multidisciplinary

Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations

Lucy F. Yang et al.

Summary: This review discusses the discovery process of aptamers, known as systematic evolution of ligands by exponential enrichment (SELEX), and their applications in biosensors and separations. Aptamers, with similar binding affinity and specificity as antibodies, have shown great potential in various fields. They have been utilized in biosensors for virus detection, such as SARS-CoV-2, and in separations for purifying specific molecules or cell types.

CHEMICAL SCIENCE (2023)

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Article Medicine, Research & Experimental

Enhanced molecular dynamic simulation studies unravel long-range effects caused by sequence variations and partner binding in RNA aptamers

Ida Autiero et al.

Summary: Intrinsic flexibility and structural modularity are common features of RNA molecules. This study used enhanced molecular dynamics simulations to investigate the effects of rigidifying RNA through complexation with high-affinity partners. The results showed that modifications in the Fab binding site significantly increased local flexibility and affected mobility in distant regions. The effectiveness of using REMD analyses to understand RNA flexibility was further demonstrated by reproducing important events in the NF-KB RNA aptamer. This technique could complement experimental data and guide the rational design of nucleic acid therapeutics.

MOLECULAR THERAPY-NUCLEIC ACIDS (2023)

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Article Biochemistry & Molecular Biology

AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

Mihaly Varadi et al.

Summary: The AlphaFold Database Protein Structure Database (AlphaFold DB) has expanded significantly since its initial release in 2021, now containing over 214 million predicted protein structures. Powered by the AlphaFold2 artificial intelligence (AI) system, the database has integrated its predictions into primary data resources such as PDB, UniProt, Ensembl, InterPro, and MobiDB. This manuscript details the enhancements made to data archiving, including the addition of model organisms, global health proteomes, Swiss-Prot integration, and curated protein datasets. The access mechanisms of AlphaFold DB, from direct file access to advanced queries using Google Cloud Public Datasets, are also discussed, along with improvements and added services since its release, such as enhancements to the Predicted Aligned Error viewer and the 3D viewer customization options.

NUCLEIC ACIDS RESEARCH (2023)

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Review Biochemical Research Methods

Protein-RNA interaction prediction with deep learning: structure matters

Junkang Wei et al.

Summary: Protein-RNA interactions play a vital role in cellular activities. Previous computational methods heavily rely on sequence data due to the lack of protein structure data. However, the emergence of AlphaFold is set to revolutionize protein-RNA interaction prediction. In this review, we provide a comprehensive overview of the field, covering binding site and binding preference prediction, as well as commonly used datasets, features, and models. We also discuss potential challenges and opportunities in this area.

BRIEFINGS IN BIOINFORMATICS (2022)

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Review Pharmacology & Pharmacy

Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing

Francesc X. Ruiz et al.

Summary: Infection with HIV and HBV are major public health problems affecting millions of people globally. The polymerases from both viruses are common drug targets, with drugs like emtricitabine and lamivudine being widely used inhibitors, but details of their binding have remained unknown.

DRUG DISCOVERY TODAY (2022)

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Article Biochemistry & Molecular Biology

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Mihaly Varadi et al.

Summary: AlphaFold DB is an openly accessible database with high-accuracy protein-structure predictions, powered by DeepMind's AlphaFold v2.0. It provides programmatic access to a vast number of predicted structures and is expanding to cover more sequences.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biophysics

Development of a DNA aptamer that binds to the complementarity-determining region of therapeutic monoclonal antibody and affinity improvement induced by pH-change for sensitive detection

Taro Saito et al.

Summary: A novel anti-idiotype aptamer A14#1 with extraordinary specificity against the anti-vascular endothelial growth factor therapeutic mAb, bevacizumab, was developed. The affinity of A14#1 to bevacizumab markedly increased at pH 4.7, enabling it to be potentially useful for therapeutic drug measurement as a novel ligand of bevacizumab.

BIOSENSORS & BIOELECTRONICS (2022)

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Editorial Material Biochemistry & Molecular Biology

Aptamers: Functional-Structural Studies and Biomedical Applications

Romualdo Troisi et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

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Article Biochemistry & Molecular Biology

Structural Basis for Fluorescence Activation by Pepper RNA

Huw C. Rees et al.

Summary: Using antibody-assisted crystallography, researchers determined the crystal structures of Pepper RNA bound to HBC, revealing that Pepper utilizes a unique base-quadruplemiddotbase-triple stack to bind to HBC. This research provides important insights into the binding mechanism between the Pepper aptamer and HBC.

ACS CHEMICAL BIOLOGY (2022)

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Article Multidisciplinary Sciences

Discovery of small molecules that target a tertiary-structured RNA

Elena Menichelli et al.

Summary: There is growing interest in using small molecules to target disease-relevant RNAs in therapeutic intervention. However, the understanding of structure-activity relationships in pursuing RNA targets is limited. This study identified several unique compounds through high-throughput screening that bind to a well-studied RNA structure, the theophylline aptamer, with significantly higher affinity than theophylline itself. The atomic-resolution X-ray crystal structures of these compounds revealed the rigidity of the RNA binding pocket and the potential for other ligands to bind more tightly. These findings suggest that the same approaches used for protein drug discovery can also be applied to RNA.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Article Medicine, Research & Experimental

A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers

Romualdo Troisi et al.

Summary: This article discusses the advantages and disadvantages of oligonucleotide aptamers and proposes strategies for improvement. Crystallographic analysis of an engineered oligonucleotide in complex with thrombin reveals that terminal modifications enhance the interaction with thrombin, thereby expanding its potential.

MOLECULAR THERAPY-NUCLEIC ACIDS (2022)

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Article Chemistry, Multidisciplinary

Discovery of a Transferrin Receptor 1-Binding Aptamer and Its Application in Cancer Cell Depletion for Adoptive T-Cell Therapy Manufacturing

Emmeline L. Cheng et al.

Summary: This study reports the identification of a novel high-affinity DNA aptamer, tJBA8.1, that binds transferrin receptor 1 (TfR1). The aptamer was found to effectively deplete B lymphoma cells from peripheral blood mononuclear cells with minimal impact on the composition of healthy immune cells. This research provides a facile, universal, and inexpensive approach for safe manufacturing of adoptive T-cell therapies.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

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Article Multidisciplinary Sciences

Cryo-EM structures of wild-type and E138K/M184I mutant HIV-1 RT/DNA complexed with inhibitors doravirine and rilpivirine

Abhimanyu K. Singh et al.

Summary: A protocol for rapid structure determination of HIV-1 reverse transcriptase (RT) complexes by cryo-electron microscopy (cryo-EM) has been optimized. Six structures of RT complexes with nonnucleoside inhibitors were determined, revealing important differences in structure and conformation. These differences have implications for understanding drug resistance mechanisms and drug design.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Article Multidisciplinary Sciences

Functional selectivity of insulin receptor revealed by aptamer-trapped receptor structures

Junhong Kim et al.

Summary: Here, the authors determine the structures of insulin receptor bound to aptamers and provide a basis for the selective activation or allosteric regulation of the insulin receptor.

NATURE COMMUNICATIONS (2022)

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Editorial Material Medicine, Research & Experimental

Minding the gap: Unlocking the therapeutic potential of aptamers and making up for lost time

Annalisa Di Ruscio et al.

MOLECULAR THERAPY-NUCLEIC ACIDS (2022)

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Article Biochemistry & Molecular Biology

Molecular dynamics simulations of human α-thrombin in different structural contexts: evidence for an aptamer-guided cooperation between the two exosites

Romualdo Troisi et al.

Summary: This study utilized molecular dynamics simulations to investigate the dynamic interactions of thrombin with aptamers TBA and HD22_27mer in binary/ternary complexes, revealing the mechanism of stabilization of these complexes in a crystal-free environment. The dynamics analysis indicated a communication between the exosites in different thrombin binding states, providing insights into the cooperativity of TBA/HD22_27mer binding experimentally detected.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

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Review Pharmacology & Pharmacy

G-quadruplex-based aptamers targeting human thrombin: Discovery, chemical modifications and antithrombotic effects

Claudia Riccardi et al.

Summary: Research on DNA aptamers targeting thrombin began in 1992, with TBA being the most well-characterized aptamer. However, unmodified aptamers exhibit limited pharmacokinetic properties, leading to the exploration of chemical modifications to improve their biological performance.

PHARMACOLOGY & THERAPEUTICS (2021)

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Article Immunology

Inhibition of the Complement Alternative Pathway by Chemically Modified DNA Aptamers That Bind with Picomolar Affinity to Factor B

Xin Xu et al.

Summary: The complement system is crucial for innate immunity, but improper activation can lead to inflammatory diseases. This study identified and characterized two DNA aptamers that inhibit the formation of the AP C3 convertase by binding to the proprotease factor B (FB), demonstrating potent AP inhibition and expanding the pipeline of FB-binding molecules.

JOURNAL OF IMMUNOLOGY (2021)

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Review Biochemistry & Molecular Biology

Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands

Romualdo Troisi et al.

Summary: This study investigates the structural determinants of thrombin partnerships with various ligands, focusing on the interaction between thrombin and exosite ligands, especially the specificity of thrombin binding to aptamers. The research reveals new insights into the design of thrombin inhibitors and the interface area between thrombin and exosite ligands.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Medicine, Research & Experimental

Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12

Igor Smirnov et al.

Summary: The study investigates the enhancement of recognition interface between thrombin-binding aptamer HD1 (TBA) and thrombin by adding chemically modified side chains to selected nucleotide residues. The modified variants showed increased affinity and anticoagulant activity, with crystal structures revealing the importance of non-equivalent binding modes in determining affinity characteristics. This approach of extending the recognition surface between protein and modified aptamers holds promise for improving aptamer ligand characteristics.

MOLECULAR THERAPY-NUCLEIC ACIDS (2021)

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Article Biochemistry & Molecular Biology

Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA

Xiaoming Ren et al.

Summary: Vertebrate organisms use protein receptors to recognize pathogenic molecules as an early warning system for infection. RIG-I, an important receptor for detecting RNA viruses, can lead to disease when dysregulated. A high affinity RIG-I antagonist was developed in this study, showing potential for generating immunomodulatory drugs and mechanistic tool compounds.

JOURNAL OF MOLECULAR BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry

Chelsy Chesterman et al.

Summary: This study demonstrates the successful introduction of synthetic symmetry into protein crystallization samples using engineered Dabs, which increased the success rate of target protein crystallization. The high-resolution structure of the Dab-RT-aptamer complex was determined, showcasing the potential of this strategy for enabling the crystallization of bound proteins.

STRUCTURE (2021)

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Article Multidisciplinary Sciences

Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening

Abhimanyu K. Singh et al.

Summary: The authors discovered a transient P-pocket created by HIV reverse transcriptase while sliding over a DNA substrate and developed a cryo-EM platform for lead optimization. By screening 300 drug-like fragments, they identified two leads that bind to the P-pocket, which is resilient to drug-resistance mutations and composed of structural elements from polymerase active site, primer grip, and template-primer. An engineered RT/DNA aptamer complex was utilized to trap the transient P-pocket and structures of the RT/DNA complex in the presence of an inhibitory fragment were determined.

NATURE COMMUNICATIONS (2021)

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Review Biology

Recent Progress and Opportunities for Nucleic Acid Aptamers

Jonghoe Byun

Summary: Aptamers, short nucleic acid sequences capable of specific molecular binding, have shown significant potential in therapeutics and diagnostics. Despite challenges in clinical trials, novel technologies and advancements are fueling hope in the field of aptamers.

LIFE-BASEL (2021)

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Review Biochemistry & Molecular Biology

Overview of the Therapeutic Potential of Aptamers Targeting Coagulation Factors

Max Liu et al.

Summary: Aptamers are single-stranded DNA or RNA sequences that exhibit high specificity and affinity in binding target molecules. They are non-immunogenic, easier to synthesize and modify, and can bind targets with greater affinity, making them a promising therapeutic candidate for treating various conditions. Active research is ongoing in developing aptamers to target blood coagulation factors, with potential applications in treating cardiovascular diseases, blood disorders, and cancers. Although no aptamers targeting blood coagulation factors have been approved for clinical use, several have shown promise in clinical trials and preclinical studies.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Review Biochemistry & Molecular Biology

Structural Biology for the Molecular Insight between Aptamers and Target Proteins

Ning Zhang et al.

Summary: Aptamers show promise as therapeutic and diagnostic agents for various diseases due to their high affinity and specificity. Structural studies and modification strategies are crucial for understanding and optimizing the interactions between aptamers and target proteins. Challenges in resolving aptamer-protein complex structures still exist, but advancements in methodologies could facilitate the development of aptamer-based therapeutics.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Review Biochemistry & Molecular Biology

Artificial Intelligence in Aptamer-Target Binding Prediction

Zihao Chen et al.

Summary: Aptamers, short nucleic acid molecules, show promise as antibody alternatives for diagnostics and therapeutics due to their unique features. The SELEX process for aptamer selection is time-consuming, calling for artificial intelligence assistance in candidate identification. Machine/deep learning methods offer potential for predicting aptamer-target binding in a more efficient manner.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Biochemistry & Molecular Biology

Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human α-thrombin

Romualdo Troisi et al.

Summary: This study investigates the simultaneous binding of two aptamers, NU172 and HD22, to human alpha-thrombin using a structural and dynamics approach. The crystal structure of the ternary complex formed by thrombin with NU172 and HD22_27mer provides insights into the cooperative binding at the two exosites and inspires the design of novel bivalent thrombin inhibitors. The study demonstrates a clear evidence of the synergic action of the two aptamers, with the binding of one aptamer influencing the flexibility and conformation of the other exosite.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2021)

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Review Biochemistry & Molecular Biology

Identification and Engineering of Aptamers for Theranostic Application in Human Health and Disorders

Debleena Basu et al.

Summary: Aptamers are short sequences of synthetic oligonucleotides that can bind specifically to their target with similar or higher sensitivity compared to antibodies. The in-vitro selection process, known as SELEX, involves a combination of chemistry and molecular biology. Chemical modifications are made to enhance stability in biofluids, with a focus on maintaining sensitivity and specificity. Aptamer applications have expanded beyond in-vitro systems to include molecular imaging for disease pathology and treatment.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Review Biotechnology & Applied Microbiology

Systematic Evolution of Ligands by Exponential Enrichment Technologies and Aptamer-Based Applications: Recent Progress and Challenges in Precision Medicine of Infectious Diseases

Yixin Xu et al.

Summary: This review provides a comprehensive overview of the latest development of SELEX technology and focuses on the applications of aptamer-based technologies in infectious diseases, such as targeted drug-delivery, treatments, and biosensors for diagnosing. The challenges and the future development in this field of clinical application will also be discussed.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2021)

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Review Veterinary Sciences

Potential applications of aptamers in veterinary science

Solene Niederlender et al.

Summary: Aptamers are small nucleic acids capable of specifically binding to targets, offering advantages such as high specificity, low immunogenicity, and easy selection. With potential applications in veterinary science for food safety, environmental safety, diagnosis, and medical treatment, aptamers have sparked growing interest and opportunities for future development in both human and animal medicine in a One Health approach.

VETERINARY RESEARCH (2021)

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Article Biochemistry & Molecular Biology

DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD

Christian Klingler et al.

FASEB JOURNAL (2020)

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Article Hematology

The development and characterization of a long acting anti-thrombotic von Willebrand factor (VWF) aptamer

Shuhao Zhu et al.

JOURNAL OF THROMBOSIS AND HAEMOSTASIS (2020)

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THE PROTEIN-IMAGING TECHNIQUE TAKING OVER STRUCTURAL BIOLOGY

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NATURE (2020)

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Article Biochemistry & Molecular Biology

The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex

Florian C. Grau et al.

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Development and structural determination of an anti-PrPC aptamer that blocks pathological conformational conversion of prion protein

Tsukasa Mashima et al.

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Current Perspectives on Aptamers as Diagnostic Tools and Therapeutic Agents

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Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer

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Evolution of abiotic cubane chemistries in a nucleic acid aptamer allows selective recognition of a malaria biomarker

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Integrative structural biology studies of HIV-1 reverse transcriptase binding to a high-affinity DNA aptamer

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Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding

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The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition

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Aptamers targeting cell surface proteins

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Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass

Ruwan Gunaratne et al.

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Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography

Deepak Koirala et al.

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Article Biochemistry & Molecular Biology

Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity

Rafal Dolot et al.

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Structure of an RNA Aptamer that Can Inhibit HIV-1 by Blocking Rev-Cognate RNA (RRE) Binding and Rev-Rev Association

Altaira D. Dearborn et al.

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HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir

Yoshiaki Yasutake et al.

SCIENTIFIC REPORTS (2018)

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Article Biochemistry & Molecular Biology

Several structural motifs cooperate in determining the highly effective anti-thrombin activity of NU172 aptamer

Romualdo Troisi et al.

NUCLEIC ACIDS RESEARCH (2018)

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Article Multidisciplinary Sciences

Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif

Sandip A. Shelke et al.

NATURE COMMUNICATIONS (2018)

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Review Chemistry, Analytical

Investigations on the interface of nucleic acid aptamers and binding targets

Shundong Cai et al.

ANALYST (2018)

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Review Biotechnology & Applied Microbiology

Aptamers as targeted therapeutics: current potential and challenges

Jiehua Zhou et al.

NATURE REVIEWS DRUG DISCOVERY (2017)

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Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers

Andrea Pica et al.

NUCLEIC ACIDS RESEARCH (2017)

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Article Multidisciplinary Sciences

Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling

Xiaoming Ren et al.

NATURE COMMUNICATIONS (2017)

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Genomic RNA folding mediates assembly of human parechovirus

Shabih Shakeel et al.

NATURE COMMUNICATIONS (2017)

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Article Biochemistry & Molecular Biology

Exosite 2-Directed Ligands Attenuate Protein C Activation by the Thrombin-Thrombomodulin Complex

Kai Chen et al.

BIOCHEMISTRY (2017)

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Article Biochemistry & Molecular Biology

Different duplex/quadruplex junctions determine the properties of anti-thrombin aptamers with mixed folding

Irene Russo Krauss et al.

NUCLEIC ACIDS RESEARCH (2016)

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Article Biochemistry & Molecular Biology

Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer

Matthew T. Miller et al.

PROTEIN SCIENCE (2016)

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Article Biochemistry & Molecular Biology

Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet

Kalyan Das et al.

ACS CHEMICAL BIOLOGY (2016)

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Article Biochemistry & Molecular Biology

Embracing proteins: structural themes in aptamer-protein complexes

Amy D. Gelinas et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2016)

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Review Biochemistry & Molecular Biology

Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods

Xing Du et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2016)

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Article Biochemistry & Molecular Biology

Structural basis for specific inhibition of Autotaxin by a DNA aptamer

Kazuki Kato et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)

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Article Biochemistry & Molecular Biology

Evoking picomolar binding in RNA by a single phosphorodithioate linkage

N. Dinuka Abeydeera et al.

NUCLEIC ACIDS RESEARCH (2016)

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Exploring the role of the alpha-carboxyphosphonate moiety in the HIV-RT activity of alpha-carboxy nucleoside phosphonates

Nicholas D. Mullins et al.

ORGANIC & BIOMOLECULAR CHEMISTRY (2016)

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Article Biochemistry & Molecular Biology

Structural basis for specific inhibition of Autotaxin by a DNA aptamer

Kazuki Kato et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)

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Article Multidisciplinary Sciences

Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition

Sung-Jin Choi et al.

SCIENTIFIC REPORTS (2016)

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Review Biochemistry & Molecular Biology

Aptamer-nanoparticle complexes as powerful diagnostic and therapeutic tools

Hunho Jo et al.

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Review Chemistry, Medicinal

Peptide Aptamers: Development and Applications

Sergey Reverdatto et al.

CURRENT TOPICS IN MEDICINAL CHEMISTRY (2015)

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Aptamers and Their Applications in Nanomedicine

Hongguang Sun et al.

SMALL (2015)

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Article Biochemistry & Molecular Biology

Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor

Thale C. Jarvis et al.

STRUCTURE (2015)

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Review Virology

Aptamers in Diagnostics and Treatment of Viral Infections

Tomasz Wandtke et al.

VIRUSES-BASEL (2015)

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Article Multidisciplinary Sciences

Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer

Laure Yatime et al.

NATURE COMMUNICATIONS (2015)

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Article Multidisciplinary Sciences

Crystal structure of a mirror-image L-RNA aptamer (Spiegelmer) in complex with the natural L-protein target CCL2

Dominik Oberthuer et al.

NATURE COMMUNICATIONS (2015)

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Article Cell Biology

Structural Basis for Molecular Discrimination by a 3′,3′-cGAMP Sensing Riboswitch

Aiming Ren et al.

CELL REPORTS (2015)

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A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore

Hao Huang et al.

NATURE CHEMICAL BIOLOGY (2014)

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Article Biochemistry & Molecular Biology

Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition

Tomohiko Hayashi et al.

NUCLEIC ACIDS RESEARCH (2014)

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Article Biochemistry & Molecular Biology

Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis

Milya Davlieva et al.

NUCLEIC ACIDS RESEARCH (2014)

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Article Biochemistry & Molecular Biology

An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates

Camille S. Padlan et al.

RNA (2014)

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Review Physics, Applied

Devices and approaches for generating specific high-affinity nucleic acid aptamers

Kylan Szeto et al.

APPLIED PHYSICS REVIEWS (2014)

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Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer

Irene Russo Krauss et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2013)

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Article Biochemistry & Molecular Biology

Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer

Andrea Pica et al.

FEBS JOURNAL (2013)

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Article Biochemistry & Molecular Biology

Ligand Binding to Anion-binding Exosites Regulates Conformational Properties of Thrombin

Marina V. Malovichko et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2013)

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Article Biochemistry & Molecular Biology

Anti-prion activity of an RNA aptamer and its structural basis

Tsukasa Mashima et al.

NUCLEIC ACIDS RESEARCH (2013)

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Article Multidisciplinary Sciences

Structural basis for discriminatory recognition of Plasmodium lactate dehydrogenase by a DNA aptamer

Yee-Wai Cheung et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

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Article Biochemistry & Molecular Biology

Structural and Biochemical Characterization of Linear Dinucleotide Analogues Bound to the c-di-GMP-I Aptamer

Kathryn D. Smith et al.

BIOCHEMISTRY (2012)

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Review Biochemistry & Molecular Biology

Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

Vincent J. B. Ruigrok et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2012)

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Article Biochemistry & Molecular Biology

Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq

Tatsuhiko Someya et al.

NUCLEIC ACIDS RESEARCH (2012)

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Article Biochemistry & Molecular Biology

High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity

Irene Russo Krauss et al.

NUCLEIC ACIDS RESEARCH (2012)

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Article Multidisciplinary Sciences

Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets

Douglas R. Davies et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

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Article Biochemistry & Molecular Biology

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops

Nathan J. Baird et al.

RNA (2012)

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Article Biochemistry & Molecular Biology

Molecular Mechanism for Inhibition of G Protein-Coupled Receptor Kinase 2 by a Selective RNA Aptamer

Valerie M. Tesmer et al.

STRUCTURE (2012)

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Review Microbiology

Aptamers in virology: recent advances and challenges

Jennifer M. Binning et al.

FRONTIERS IN MICROBIOLOGY (2012)

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Article Chemistry, Analytical

Measurement of Aptamer-Protein Interactions with Back-Scattering Interferometry

Ian R. Olmsted et al.

ANALYTICAL CHEMISTRY (2011)

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Article Biochemistry & Molecular Biology

A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination

Yelena Koldobskaya et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)

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Article Biochemistry & Molecular Biology

Thrombin-aptamer recognition: a revealed ambiguity

Irene Russo Krauss et al.

NUCLEIC ACIDS RESEARCH (2011)

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Article Biochemistry & Molecular Biology

Structural and Biochemical Determinants of Ligand Binding by the c-di-GMP Riboswitch

Kathryn D. Smith et al.

BIOCHEMISTRY (2010)

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Review Biotechnology & Applied Microbiology

Aptamers as therapeutics

Anthony D. Keefe et al.

NATURE REVIEWS DRUG DISCOVERY (2010)

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Article Biochemistry & Molecular Biology

Conformational plasticity of RNA for target recognition as revealed by the 2.15 Å crystal structure of a human IgG-aptamer complex

Yusuke Nomura et al.

NUCLEIC ACIDS RESEARCH (2010)

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Article Biochemistry & Molecular Biology

Biophysical Investigation of GpIbα Binding to Thrombin Anion Binding Exosite II

T. Michael Sabo et al.

BIOCHEMISTRY (2009)

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Therapeutic antibodies: successes, limitations and hopes for the future

Patrick Chames et al.

BRITISH JOURNAL OF PHARMACOLOGY (2009)

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Article Biochemistry & Molecular Biology

Long Range Communication between Exosites 1 and 2 Modulates Thrombin Function

Nicolas S. Petrera et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2009)

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Article Biochemistry & Molecular Biology

Structural basis of ligand binding by a c-di-GMP riboswitch

Kathryn D. Smith et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

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Article Biochemistry & Molecular Biology

A Structural Explanation for the Antithrombotic Activity of ARC1172, a DNA Aptamer that Binds von Willebrand Factor Domain A1

Ren-Huai Huang et al.

STRUCTURE (2009)

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Article Biochemistry & Molecular Biology

Structural Basis for Specific, High-Affinity Tetracycline Binding by an In Vitro Evolved Aptamer and Artificial Riboswitch

Hong Xiao et al.

CHEMISTRY & BIOLOGY (2008)

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Article Biochemistry & Molecular Biology

Crystal structure of an RNA aptamer bound to thrombin

Stephen B. Long et al.

RNA (2008)

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Article Biochemistry & Molecular Biology

DNA mimicry by a high-affinity anti-NF-κB RNA aptamer

Nicholas J. Reiter et al.

NUCLEIC ACIDS RESEARCH (2008)

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Review Multidisciplinary Sciences

Reaching for high-hanging fruit in drug discovery at protein-protein interfaces

James A. Wells et al.

NATURE (2007)

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Review Biochemistry & Molecular Biology

Inference of macromolecular assemblies from crystalline state

Evgeny Krissinel et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

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Article Biochemistry & Molecular Biology

Conformational analysis of γ′ peptide (410-427) interactions with thrombin anion binding exosite II

T. Michael Sabo et al.

BIOCHEMISTRY (2006)

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Review Biotechnology & Applied Microbiology

Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease

EWM Ng et al.

NATURE REVIEWS DRUG DISCOVERY (2006)

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Article Biochemistry & Molecular Biology

Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs

H Kettenberger et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2006)

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Article Biochemistry & Molecular Biology

Thrombomodulin tightens the thrombin active site loops to promote protein C activation

JR Koeppe et al.

BIOCHEMISTRY (2005)

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Article Biochemistry & Molecular Biology

The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: Further challenges in the modeling of ligand-RNA interactions

WT Horn et al.

RNA (2004)

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Article Multidisciplinary Sciences

Crystal structure of NF-κB (p50)2 complexed to a high-affinity RNA aptamer

DB Huang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

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Article Biochemistry & Molecular Biology

Protein-RNA interactions: a structural analysis

S Jones et al.

NUCLEIC ACIDS RESEARCH (2001)

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