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Oligonucleotide Aptamers: Emerging Affinity Probes For Bioanalytical Mass Spectrometry And Biomarker Discovery
Published 2015 · Chemistry
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Selective isolation of biologically important molecules and their functional characterization is one of the primary goals of bioanalytical chemistry. Several different affinity tools such as antibodies, affimers, nanobodies, and DARPins have been explored to achieve these goals. In recent years, oligonucleotide based affinity tools called aptamers have become progressively attractive and the research in this area has seen an exponential increase. Aptamer probes have been explored in many different areas of bioanalytical chemistry such as electrochemical and optical biosensor development, targeted drug delivery, logic gates, DNA nanotechnology, and point of care diagnostics. However aptamers are still largely overlooked in mass spectrometry (MS) and biomarker discovery. After the completion of the human genome project, the focus has shifted towards functional genomics and to understand the living systems by deciphering the functions of proteins and metabolites. Therefore identification and functional characterization of these molecules are of outmost importance. Although identification of isolated biomolecules and analysis of simple biological mixtures using MS have become relatively simple, the power of MS gradually decreases as the complexity of biological mixtures increases. Therefore the development of selective and targeted approaches is at the forefront of mass spectrometry. Aptamers have great potential in affinity mass spectrometry to improve selectivity, specificity and throughput. Herein, bioanalytical mass spectrometry and biomarker discovery applications of aptamers will be reviewed.
This paper references
Antimicrobial aptamers for detection and inhibition of microbial pathogen growth.
V. C. Özalp (2013)
Elucidating Novel Serum Biomarkers Associated with Pulmonary Tuberculosis Treatment
M. A. De Groote (2013)
Targeting cancer cells using aptamers: cell-SELEX approach and recent advancements
J. Barman (2015)
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
C. Tuerk (1990)
Protein Signature of Lung Cancer Tissues
Michael R. Mehan (2012)
Aptamer/ISET-MS: a new affinity-based MALDI technique for improved detection of biomarkers.
S. Lee (2014)
Functionalized nanoparticles and nanostructured surfaces for surface-assisted laser desorption/ionization mass spectrometry.
R. Arakawa (2010)
The Cytosolic Domain of Protein-tyrosine Kinase 7 (PTK7), Generated from Sequential Cleavage by a Disintegrin and Metalloprotease 17 (ADAM17) and γ-Secretase, Enhances Cell Proliferation and Migration in Colon Cancer Cells*
Hye-Won Na (2012)
Kinetic binding analysis of aptamers targeting HIV-1 proteins by a combination of a microbalance array and mass spectrometry (MAMS).
T. Gronewold (2009)
Structural features of the L-argininamide-binding DNA aptamer studied with ESI-FTMS.
X. Guo (2006)
Strong anion exchange for studying protein—dna interactions by H/D exchange mass spectrometry
J. Sperry (2008)
Alkaline phosphatase ALPPL-2 is a novel pancreatic carcinoma-associated protein.
Pooja Dua (2013)
Targeting the Variable Surface of African Trypanosomes with Variant Surface Glycoprotein-Specific, Serum-Stable RNA Aptamers
Mihaela Lorger (2003)
Analysis of adenosine triphosphate and glutathione through gold nanoparticles assisted laser desorption/ionization mass spectrometry.
Y. Huang (2007)
Targeted metabolomics in the expanded newborn screening for inborn errors of metabolism.
Emanuela Scolamiero (2015)
Aptamer-based multiplexed proteomic technology for biomarker discovery
L. Gold (2010)
PTK 7 Is a Transforming Gene and Prognostic Marker for Breast Cancer and Nodal Metastasis Involvement
Silvia Gärtner (2014)
High-density micro-arrays for mass spectrometry.
P. Urban (2010)
Small-molecule analysis with silicon-nanoparticle-assisted laser desorption/ionization mass spectrometry.
Xiujuan Wen (2007)
Site-directed antibody immobilization techniques for immunosensors.
A. Makaraviciute (2013)
Characterization and target identification of a DNA aptamer that labels pluripotent stem cells
Zhonggang Hou (2015)
A repository of assays to quantify 10,000 human proteins by SWATH-MS
G. Rosenberger (2014)
Protein microarray technology: how far off is routine diagnostics?
M. Cretich (2014)
Multiplexed mass spectrometric immunoassay in biomarker research: a novel approach to the determination of a myocardial infarct.
U. Kiernan (2006)
A meta-analysis of lung cancer gene expression identifies PTK7 as a survival gene in lung adenocarcinoma.
R. Chen (2014)
Development of DNA aptamers using Cell-SELEX
K. Sefah (2010)
Aptamer-facilitated biomarker discovery (AptaBiD).
M. Berezovski (2008)
Application of locked nucleic acids to improve aptamer in vivo stability and targeting function.
K. Schmidt (2004)
Early Detection of Malignant Pleural Mesothelioma in Asbestos-Exposed Individuals with a Noninvasive Proteomics-Based Surveillance Tool
R. Ostroff (2012)
High affinity ligands from in vitro selection: complex targets.
K. Morris (1998)
Kinetic and Stoichiometric Characterisation of Streptavidin‐Binding Aptamers
Vincent J. B. Ruigrok (2012)
The chemical biology of aptamers.
G. Mayer (2009)
Development of a MALDI-TOF MS strategy for the high-throughput analysis of biomarkers: on-target aptamer immobilization and laser-accelerated proteolysis.
Xueyang Zhang (2013)
Protein engineering for directed immobilization.
E. Steen Redeker (2013)
Microbead‐based affinity chromatography chip using RNA aptamer modified with photocleavable linker
S. Cho (2004)
Aptamers recognizing glycosylated hemagglutinin expressed on the surface of vaccinia virus-infected cells.
Parag Anil Parekh (2010)
Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease
Eugene W. M. Ng (2006)
Aptamers generated by Cell SELEX for biomarker discovery.
Youngmi Kim (2009)
A dual platform for selective analyte enrichment and ionization in mass spectrometry using aptamer-conjugated graphene oxide.
Basri Gulbakan (2010)
Dissecting the effect of RNA aptamer binding on the dynamics of plasminogen activator inhibitor 1 using hydrogen/deuterium exchange mass spectrometry.
M. B. Trelle (2014)
Desorption–ionization mass spectrometry on porous silicon
Jing Wei (1999)
Modern analytical techniques in metabolomics analysis.
A. Zhang (2012)
Identification of Cell Membrane Protein Stress-Induced Phosphoprotein 1 as a Potential Ovarian Cancer Biomarker Using Aptamers Selected by Cell Systematic Evolution of Ligands by Exponential Enrichment
Dimitri Van Simaeys (2014)
Aptamer-enhanced laser desorption/ionization for affinity mass spectrometry.
Lawrence W. Dick (2004)
Multiple ionization mass spectrometry strategy used to reveal the complexity of metabolomics.
A. Nordström (2008)
Aptamer-conjugated multifunctional nanoflowers as a platform for targeting, capture, and detection in laser desorption ionization mass spectrometry.
I. Ocsoy (2013)
Direct access to aptamer–protein complexes via MALDI-MS
F. Chen (2013)
Nucleic acid aptamers as high affinity ligands in biotechnology and biosensorics.
T. Smuc (2013)
Electrospray wings for molecular elephants (Nobel lecture).
J. Fenn (2003)
Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis*
L. Gillet (2012)
Nucleic acid aptamers for living cell analysis.
Xiangling Xiong (2014)
The cell polarity PTK7 receptor acts as a modulator of the chemotherapeutic response in acute myeloid leukemia and impairs clinical outcome.
T. Prebet (2010)
Tenascin-C Aptamers Are Generated Using Tumor Cells and Purified Protein*
B. Hicke (2001)
Mass spectrometry-based proteomics: existing capabilities and future directions.
T. E. Angel (2012)
Aptamer-based impedimetric sensor for bacterial typing.
Mahmoud Labib (2012)
Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness*
Y. Liu (2014)
Aptamer from whole-bacterium SELEX as new therapeutic reagent against virulent Mycobacterium tuberculosis.
F. Chen (2007)
High sensitivity and analyte capture with desorption/ionization mass spectrometry on silylated porous silicon.
S. Trauger (2004)
Nanoproteomics: a new sprout from emerging links between nanotechnology and proteomics.
Lee Jia (2013)
Mass spectrometric studies of alkali metal ion binding on thrombin-binding aptamer DNA
Eun Sun Hong (2010)
Unlocking Biomarker Discovery: Large Scale Application of Aptamer Proteomic Technology for Early Detection of Lung Cancer
R. Ostroff (2010)
Aptamer Directly Evolved from Live Cells Recognizes Membrane Bound Immunoglobin Heavy Mu Chain in Burkitt's Lymphoma Cells*S
Prabodhika Mallikaratchy (2007)
Cell-specific aptamer probes for membrane protein elucidation in cancer cells.
Dihua Shangguan (2008)
Newborn screening for lysosomal storage diseases.
M. Gelb (2015)
Applications of aptamers in cancer cell biology.
J. Phillips (2008)
Applications of Hydrogen/Deuterium Exchange MS from 2012 to 2014
Gregory F. Pirrone (2015)
Adjustable fragmentation in laser desorption/ionization from laser-induced silicon microcolumn arrays.
Y. Chen (2006)
Aptamer microarray mediated capture and mass spectrometry identification of biomarker in serum samples.
J. Ahn (2010)
In vitro selection with artificial expanded genetic information systems
K. Sefah (2013)
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
A. Bell (2009)
PTK7: a new biomarker for immunophenotypic characterization of maturing T cells and T cell acute lymphoblastic leukemia.
Guohua Jiang (2012)
Binding stoichiometry of an RNA aptamer and its transcription factor target.
L. A. Cassiday (2002)
Laser desorption ionization mass spectrometry on silicon nanowell arrays.
Basri Gulbakan (2010)
Candidate blood proteome markers of Alzheimer's disease onset and progression: a systematic review and replication study.
S. Kiddle (2014)
Insulin capture by an insulin-linked polymorphic region G-quadruplex DNA oligonucleotide.
Adam C Connor (2006)
Functionalized nanoparticles for liquid atmospheric pressure matrix-assisted laser desorption/ionization peptide analysis.
Kevin Turney (2004)
Aptamers as therapeutics
A. Keefe (2010)
In vitro selection of DNA aptamers to anthrax spores with electrochemiluminescence detection.
J. Bruno (1999)
Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons.
M. Karas (1988)
The strategy, organization, and progress of the HUPO Human Proteome Project.
Gilbert S. Omenn (2014)
Electrospray ionization of nucleic acid aptamer/small molecule complexes for screening aptamer selectivity.
K. Keller (2005)
Nanoparticle-based mass spectrometry for the analysis of biomolecules.
Cheng-Kang Chiang (2011)
Combination of a SAW-biosensor with MALDI mass spectrometric analysis.
G. Treitz (2008)
Protein Tyrosine Kinase 7 (PTK7) as a Predictor of Lymph Node Metastases and a Novel Prognostic Biomarker in Patients with Prostate Cancer
Hongtuan Zhang (2014)
DNA oligonucleotides: a model system with tunable binding strength to study monomer-dimer equilibria with electrospray ionization-mass spectrometry.
K. Barylyuk (2013)
Targeting Axl with an high-affinity inhibitory aptamer.
L. Cerchia (2012)
Photoaptamer Technology: Development of Multiplexed Microarray Protein Assays
D. Zichi (2002)
Identification of proteins bound to a thioaptamer probe on a proteomics array.
H. Wang (2006)
Single-stranded DNA aptamers that bind differentiated but not parental cells: subtractive systematic evolution of ligands by exponential enrichment.
C. Wang (2003)
Cell-specific aptamer-mediated targeted drug delivery.
J. Zhou (2011)
Disease‐specific biomarker discovery by aptamers
H. Ulrich (2009)
An aptamer based on-plate microarray for high-throughput insulin detection by MALDI-TOF MS.
Xueyang Zhang (2012)
Identification and expression of troponin T, a new marker on the surface of cultured tumor endothelial cells by aptamer ligand
M. N. Ara (2014)
Mass spectrometry-based proteomics and network biology.
A. Bensimon (2012)
Aptamers evolved from live cells as effective molecular probes for cancer study
Dihua Shangguan (2006)
Analysis of protein conformation and dynamics by hydrogen/deuterium exchange MS.
J. Engen (2009)
Generation of high-affinity DNA aptamers using an expanded genetic alphabet
M. Kimoto (2013)
Aptamers in Diagnostics and Treatment of Viral Infections
Tomasz Wandtke (2015)
Biomimetic Antireflective Silicon Nanocones Array for Small Molecules Analysis
Y. Wang (2012)
Photoaptamer arrays applied to multiplexed proteomic analysis
C. Bock (2004)
Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling
H. P. Benton (2015)
Mining the plasma proteome for cancer biomarkers
S. Hanash (2008)
Aptamers and SELEX in Chemistry & Biology.
M. Famulok (2014)
Aptamers come of age – at last
D. Bunka (2006)
Towards the development of an immuno MALDI (iMALDI) mass spectrometry assay for the diagnosis of hypertension
J. D. Reid (2010)
Combinatorial selection of high affinity RNA ligands to live African trypanosomes.
M. Homann (1999)
Aptamer-based affinity labeling of proteins.
Jan L. Vinkenborg (2012)
Biomarker discovery by proteomics: challenges not only for the analytical chemist.
P. Horvatovich (2006)
From SOMAmer-Based Biomarker Discovery to Diagnostic and Clinical Applications: A SOMAmer-Based, Streamlined Multiplex Proteomic Assay
S. Krämer (2011)
In vitro selection of RNA molecules that bind specific ligands
A. Ellington (1990)
Expanding the chemistry of DNA for in vitro selection.
Jonathan D. Vaught (2010)
Age-dependent changes in the cerebrospinal fluid proteome by slow off-rate modified aptamer array.
G. Baird (2012)
Applying mass spectrometry to study non-covalent biomolecule complexes.
F. Chen (2016)
Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry
K. Tanaka (1988)
Selection and analytical applications of aptamers binding microbial pathogens
C. Hamula (2011)
Specific capture and detection of Staphylococcus aureus with high-affinity modified aptamers to cell surface components
A. Baumstummler (2014)
Determination of thermodynamic and kinetic properties of biomolecules by mass spectrometry.
Basri Gülbakan (2015)
Systematic Evolution of a DNA Aptamer Binding to Rat Brain Tumor Microvessels
M. Blank (2001)
Enrichment and detection of rare proteins with aptamer-conjugated gold nanorods.
Emir Yasun (2012)
Discovery and development of therapeutic aptamers.
P. Bouchard (2010)
Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences.
F. Kobeissy (2014)
Protein biomarker discovery and validation: the long and uncertain path to clinical utility
N. Rifai (2006)
Affinity capture and detection of immunoglobulin E in human serum using an aptamer-modified surface in matrix-assisted laser desorption/ionization mass spectrometry.
J. Cole (2007)
Development of aptamer-conjugated magnetic graphene/gold nanoparticle hybrid nanocomposites for specific enrichment and rapid analysis of thrombin by MALDI-TOF MS.
Ya Xiong (2014)
A critical comparison of protein microarray fabrication technologies.
V. Romanov (2014)
Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins.
G. Omenn (2014)
A tenascin-C aptamer identified by tumor cell SELEX: Systematic evolution of ligands by exponential enrichment
D. Daniels (2003)
In Vitro Selection of RNA Aptamers That Bind to Cell Adhesion Receptors of Trypanosoma cruzi and Inhibit Cell Invasion*
H. Ulrich (2002)
Mass spectrometry in biomarker applications: from untargeted discovery to targeted verification, and implications for platform convergence and clinical application.
R. Smith (2012)
This paper is referenced by
An evaluation of an aptamer for use as an affinity reagent with MS: PCSK9 as an example protein.
V. Gupta (2016)
RNA aptamer capture of macromolecular complexes for mass spectrometry analysis
J. Ray (2020)
Recent Advances in the Characterization and Analysis of Therapeutic Oligonucleotides by Analytical Separation Methods Coupling with Mass Spectrometry.
Pan Su (2017)
Real-time detection of the interaction between alpha-fetoprotein and its ssDNA aptamer by dual polarization interferometry
Chenggang Shao (2018)