4.7 Review

Structural Biology for the Molecular Insight between Aptamers and Target Proteins

Related references

Note: Only part of the references are listed.
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)

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)

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)

Article Chemistry, Physical

Molecular characterization of a ghrelin-L-aptamer complex

Christina Schmidt et al.

JOURNAL OF MOLECULAR STRUCTURE (2020)

Review Biochemistry & Molecular Biology

Aptamers Chemistry: Chemical Modifications and Conjugation Strategies

Fadwa Odeh et al.

MOLECULES (2020)

Review Cell Biology

Pros and Cons of Denosumab Treatment for Osteoporosis and Implication for RANKL Aptamer Therapy

Ning Zhang et al.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2020)

Review Biochemistry & Molecular Biology

Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects

Jan P. Elskens et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Biochemistry & Molecular Biology

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

Jakub Ptacek et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

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

Steve Tuske et al.

CURRENT RESEARCH IN STRUCTURAL BIOLOGY (2020)

Article Multidisciplinary Sciences

Modified aptamers as reagents to characterize recombinant human erythropoietin products

Wojciech Jankowski et al.

SCIENTIFIC REPORTS (2020)

Article Genetics & Heredity

Aptamers as Therapeutic Agents: Has the Initial Euphoria Subsided?

S. K. Hassel et al.

MOLECULAR DIAGNOSIS & THERAPY (2019)

Article Biochemical Research Methods

Thermophoresis for characterizing biomolecular interaction

Mufarreh Asmari et al.

METHODS (2018)

Article Biotechnology & Applied Microbiology

Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass

Ruwan Gunaratne et al.

NATURE BIOTECHNOLOGY (2018)

Review Biotechnology & Applied Microbiology

Cryo-EM in drug discovery: achievements, limitations and prospects

Jean-Paul Renaud et al.

NATURE REVIEWS DRUG DISCOVERY (2018)

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)

Review Chemistry, Analytical

Investigations on the interface of nucleic acid aptamers and binding targets

Shundong Cai et al.

ANALYST (2018)

Article Biochemistry & Molecular Biology

Two stems with different characteristics and an internal loop in an RNA aptamer contribute to spermine-binding

Akihiro Oguro et al.

JOURNAL OF BIOCHEMISTRY (2017)

Article Biochemistry & Molecular Biology

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

Andrea Pica et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemical Research Methods

Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry

Jiang Zhang et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2017)

Article Chemistry, Analytical

Selection and characterization of DNA aptamers against the steroid testosterone

Vasso Skouridou et al.

MICROCHIMICA ACTA (2017)

Article Biochemistry & Molecular Biology

The SMX DNA Repair Tri-nuclease

Haley D. M. Wyatt et al.

MOLECULAR CELL (2017)

Article Biochemical Research Methods

Preparation of glycoconjugates from unprotected carbohydrates for protein-binding studies

Christian T. Hjuler et al.

NATURE PROTOCOLS (2017)

Article Multidisciplinary Sciences

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

Clemens Entzian et al.

JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2017)

Article Biochemistry & Molecular Biology

Applications of NMR to structure determination of RNAs large and small

Ravi P. Barnwal et al.

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2017)

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)

Article Chemistry, Analytical

Surface-Enhanced Raman Spectroscopy Biosensing: In Vivo Diagnostics and Multimodal Imaging

Anne-Isabelle Henry et al.

ANALYTICAL CHEMISTRY (2016)

Article Biochemistry & Molecular Biology

Embracing proteins: structural themes in aptamer-protein complexes

Amy D. Gelinas et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2016)

Review Biochemistry & Molecular Biology

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

Xing Du et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2016)

Article Biochemistry & Molecular Biology

Structural basis for specific inhibition of Autotaxin by a DNA aptamer

Kazuki Kato et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Evoking picomolar binding in RNA by a single phosphorodithioate linkage

N. Dinuka Abeydeera et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Biochemistry & Molecular Biology

Trends in the Design and Development of Specific Aptamers Against Peptides and Proteins

Maryam Tabarzad et al.

PROTEIN JOURNAL (2016)

Article Biochemistry & Molecular Biology

Structural basis for specific inhibition of Autotaxin by a DNA aptamer

Kazuki Kato et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)

Article Multidisciplinary Sciences

G-quadruplex aptamer targeting Protein A and its capability to detect Staphylococcus aureus demonstrated by ELONA

Regina Stoltenburg et al.

SCIENTIFIC REPORTS (2016)

Article Physics, Atomic, Molecular & Chemical

Native top-down mass spectrometry for the structural characterization of human hemoglobin

Jiang Zhang et al.

EUROPEAN JOURNAL OF MASS SPECTROMETRY (2015)

Article Multidisciplinary Sciences

Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly

Andrew P. AhYoung et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Review Biochemistry & Molecular Biology

How cryo-EM is revolutionizing structural biology

Xiao-Chen Bai et al.

TRENDS IN BIOCHEMICAL SCIENCES (2015)

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)

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)

Article Biochemistry & Molecular Biology

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

Hao Huang et al.

NATURE CHEMICAL BIOLOGY (2014)

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)

Article Biochemical Research Methods

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)

Article Chemistry, Multidisciplinary

Near-Field Enhanced Plasmonic-Magnetic Bifunctional Nanotubes for Single Cell Bioanalysis

Xiaobin Xu et al.

ADVANCED FUNCTIONAL MATERIALS (2013)

Article Chemistry, Medicinal

Synthesis, characterization and in vitro activity of thrombin-binding DNA aptamers with triazole internucleotide linkages

Anna M. Varizhuk et al.

EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (2013)

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)

Article Biochemistry & Molecular Biology

Staphylococcus aureus Uses a Novel Multidomain Receptor to Break Apart Human Hemoglobin and Steal Its Heme

Thomas Spirig et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2013)

Article Biochemical Research Methods

Biomarker Discovery for Early Detection of Hepatocellular Carcinoma in Hepatitis C-infected Patients

Mehnaz G. Mustafa et al.

MOLECULAR & CELLULAR PROTEOMICS (2013)

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)

Article Biophysics

G-Quadruplex and i-Motif Are Mutually Exclusive in ILPR Double-Stranded DNA

Soma Dhakal et al.

BIOPHYSICAL JOURNAL (2012)

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)

Article Chemistry, Multidisciplinary

Analyte-Driven Switching of DNA Charge Transport: De Novo Creation of Electronic Sensors for an Early Lung Cancer Biomarker

Jason M. Thomas et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

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)

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)

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)

Article Biochemistry & Molecular Biology

Thrombin-aptamer recognition: a revealed ambiguity

Irene Russo Krauss et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Chemistry, Multidisciplinary

Optical Thermophoresis for Quantifying the Buffer Dependence of Aptamer Binding

Philipp Baaske et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)

Article Biochemistry & Molecular Biology

In vitro lectin-mediated selection and characterization of rHuEPO-α-binding ssDNA aptamers

Zhaoyang Zhang et al.

BIOORGANIC & MEDICINAL CHEMISTRY (2010)

Article Medicine, Research & Experimental

Anticoagulant Effects of Thioanalogs of Thrombin-Binding DNA-Aptamer and Their Stability in the Plasma

G. E. Pozmogova et al.

BULLETIN OF EXPERIMENTAL BIOLOGY AND MEDICINE (2010)

Review Biochemistry & Molecular Biology

From Anionic to Cationic alpha-Anomeric Oligodeoxynucleotides

Francois Morvan et al.

CHEMISTRY & BIODIVERSITY (2010)

Review Medical Laboratory Technology

MCP-1: Chemoattractant with a role beyond immunity: A review

Amita Yadav et al.

CLINICA CHIMICA ACTA (2010)

Article Biotechnology & Applied Microbiology

Bioimaging of Nucleolin Aptamer-Containing 5-(N-benzylcarboxyamide)-2 '-deoxyuridine More Capable of Specific Binding to Targets in Cancer Cells

Kyue Yim Lee et al.

JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY (2010)

Article Biochemistry & Molecular Biology

Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein

Tsukasa Mashima et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biophysics

Stability and binding properties of a modified thrombin binding aptamer

Bruno Pagano et al.

BIOPHYSICAL JOURNAL (2008)

Article Biochemistry & Molecular Biology

Effect of locked-nucleic acid on a biologically active G-quadruplex. A structure-activity relationship of the thrombin aptamer

Laura Bonifacio et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2008)

Article Biochemistry & Molecular Biology

Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G

Shin Miyakawa et al.

Article Biochemistry & Molecular Biology

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

Nicholas J. Reiter et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

Multidomain targeting generates a high-affinity thrombin-inhibiting bivalent aptamer

Jens Mueller et al.

CHEMBIOCHEM (2007)

Review Biotechnology & Applied Microbiology

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

EWM Ng et al.

NATURE REVIEWS DRUG DISCOVERY (2006)

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)

Article Chemistry, Multidisciplinary

Multiple intermolecular interaction modes of positively charged residues with adenine in ATP-binding proteins

LS Mao et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

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)

Article Chemistry, Analytical

Specific aptamer-protein interaction studied by atomic force microscopy

YX Jiang et al.

ANALYTICAL CHEMISTRY (2003)

Article Multidisciplinary Sciences

RNA aptamers as reversible antagonists of coagulation factor IXa

CP Rusconi et al.

NATURE (2002)

Article Biochemistry & Molecular Biology

Cation-π/H-bond stair motifs at protein-DNA interfaces

M Rooman et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Review Biochemistry & Molecular Biology

Atomic force microscopy of macromolecular interactions

CM Yip

CURRENT OPINION IN STRUCTURAL BIOLOGY (2001)

Article Biophysics

Biomolecular interactions measured by atomic force microscopy

OH Willemsen et al.

BIOPHYSICAL JOURNAL (2000)

Article Biochemistry & Molecular Biology

Contribution of cation-π interactions to the stability of protein-DNA complexes

R Wintjens et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)

Review Multidisciplinary Sciences

Biochemistry - Adaptive recognition by nucleic acid aptamers

T Hermann et al.

SCIENCE (2000)