Fabrication and Characterization of RNA Aptamer Microarrays for the Study of Protein-aptamer Interactions with SPR Imaging

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Nov 30

PMID 17130155

Citations 30

Authors

Yuan Li

Hye Jin Lee

Robert M Corn

Affiliations

Soon will be listed here.

Abstract

RNA microarrays were created on chemically modified gold surfaces using a novel surface ligation methodology and employed in a series of surface plasmon resonance imaging (SPRI) measurements of DNA-RNA hybridization and RNA aptamer-protein binding. Various unmodified single-stranded RNA (ssRNA) oligonucleotides were ligated onto identical 5'-phosphate-terminated ssDNA microarray elements with a T4 RNA ligase surface reaction. A combination of ex situ polarization modulation FTIR measurements of the RNA monolayer and in situ SPRI measurements of DNA hybridization adsorption onto the surface were used to determine an ssRNA surface density of 4.0 x 10(12) molecules/cm2 and a surface ligation efficiency of 85 +/- 10%. The surface ligation methodology was then used to create a five-component RNA microarray of potential aptamers for the protein factor IXa (fIXa). The relative surface coverages of the different aptamers were determined through a novel enzymatic method that employed SPRI measurements of a surface RNase H hydrolysis reaction. SPRI measurements were then used to correctly identify the best aptamer to fIXa, which was previously determined from SELEX measurements. A Langmuir adsorption coefficient of 1.6 x 10(7) M(-1) was determined for fIXa adsorption to this aptamer. Single-base variations from this sequence were shown to completely destroy the aptamer-fIXa binding interaction.

Citing Articles

Aptamers Targeting Membrane Proteins for Sensor and Diagnostic Applications.

Kara N, Ayoub N, Ilgu H, Fotiadis D, Ilgu M Molecules. 2023; 28(9).

PMID: 37175137 PMC: 10180177. DOI: 10.3390/molecules28093728.

Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins.

Priest L, Peters J, Kukura P Chem Rev. 2021; 121(19):11937-11970.

PMID: 34587448 PMC: 8517954. DOI: 10.1021/acs.chemrev.1c00271.

Structural Biology for the Molecular Insight between Aptamers and Target Proteins.

Zhang N, Chen Z, Liu D, Jiang H, Zhang Z, Lu A Int J Mol Sci. 2021; 22(8).

PMID: 33920991 PMC: 8071422. DOI: 10.3390/ijms22084093.

Spotting, Transcription and Synthesis: Three Routes for the Fabrication of RNA Microarrays.

Lietard J, Somoza M Comput Struct Biotechnol J. 2019; 17:862-868.

PMID: 31321002 PMC: 6612525. DOI: 10.1016/j.csbj.2019.06.004.

High-Density RNA Microarrays Synthesized In Situ by Photolithography.

Lietard J, Ameur D, Damha M, Somoza M Angew Chem Int Ed Engl. 2018; 57(46):15257-15261.

PMID: 30187993 PMC: 6237118. DOI: 10.1002/anie.201806895.

References

Kyo M, Usui-Aoki K, Koga H . Label-free detection of proteins in crude cell lysate with antibody arrays by a surface plasmon resonance imaging technique. Anal Chem. 2005; 77(22):7115-21. DOI: 10.1021/ac050884a. View

Murphy M, Fuller S, Richardson P, Doyle S . An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Res. 2003; 31(18):e110. PMC: 203336. DOI: 10.1093/nar/gng110. View

Robertson D, Joyce G . Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature. 1990; 344(6265):467-8. DOI: 10.1038/344467a0. View

Kirby R, Cho E, Gehrke B, Bayer T, Park Y, Neikirk D . Aptamer-based sensor arrays for the detection and quantitation of proteins. Anal Chem. 2004; 76(14):4066-75. DOI: 10.1021/ac049858n. View

Proske D, Blank M, Buhmann R, Resch A . Aptamers--basic research, drug development, and clinical applications. Appl Microbiol Biotechnol. 2005; 69(4):367-74. DOI: 10.1007/s00253-005-0193-5. View

Lu M, Knickerbocker T, Cai W, Yang W, Hamers R, Smith L . Invasive cleavage reactions on DNA-modified diamond surfaces. Biopolymers. 2004; 73(5):606-13. DOI: 10.1002/bip.20007. View

BROCKMAN J, Nelson B, Corn R . Surface plasmon resonance imaging measurements of ultrathin organic films. Annu Rev Phys Chem. 2000; 51:41-63. DOI: 10.1146/annurev.physchem.51.1.41. View

Wolf L, Fullenkamp D, Georgiadis R . Quantitative angle-resolved SPR imaging of DNA-DNA and DNA-drug kinetics. J Am Chem Soc. 2005; 127(49):17453-9. DOI: 10.1021/ja056422w. View

Tuerk C, Gold L . Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990; 249(4968):505-10. DOI: 10.1126/science.2200121. View

10.

Zhong X, Leng L, Beitin A, Chen R, McDonald C, Hsiao B . Simultaneous detection of microsatellite repeats and SNPs in the macrophage migration inhibitory factor (MIF) gene by thin-film biosensor chips and application to rural field studies. Nucleic Acids Res. 2005; 33(13):e121. PMC: 1182331. DOI: 10.1093/nar/gni123. View

11.

Wallace S, Schroeder R . In vitro selection and characterization of streptomycin-binding RNAs: recognition discrimination between antibiotics. RNA. 1998; 4(1):112-23. PMC: 1369601. View

12.

Rusconi C, Scardino E, Layzer J, Pitoc G, Ortel T, Monroe D . RNA aptamers as reversible antagonists of coagulation factor IXa. Nature. 2002; 419(6902):90-4. DOI: 10.1038/nature00963. View

13.

Bock C, Coleman M, Collins B, Davis J, Foulds G, Gold L . Photoaptamer arrays applied to multiplexed proteomic analysis. Proteomics. 2004; 4(3):609-18. DOI: 10.1002/pmic.200300631. View

14.

Albert T, Norton J, Ott M, Richmond T, Nuwaysir K, Nuwaysir E . Light-directed 5'-->3' synthesis of complex oligonucleotide microarrays. Nucleic Acids Res. 2003; 31(7):e35. PMC: 152820. DOI: 10.1093/nar/gng035. View

15.

Wegner G, Lee H, Corn R . Characterization and optimization of peptide arrays for the study of epitope-antibody interactions using surface plasmon resonance imaging. Anal Chem. 2002; 74(20):5161-8. DOI: 10.1021/ac025922u. View

16.

Brody E, Gold L . Aptamers as therapeutic and diagnostic agents. J Biotechnol. 2000; 74(1):5-13. DOI: 10.1016/s1389-0352(99)00004-5. View

17.

Lee H, Wark A, Li Y, Corn R . Fabricating RNA microarrays with RNA-DNA surface ligation chemistry. Anal Chem. 2005; 77(23):7832-7. DOI: 10.1021/ac0516180. View

18.

Lyon L, Musick M, Natan M . Colloidal Au-enhanced surface plasmon resonance immunosensing. Anal Chem. 1998; 70(24):5177-83. DOI: 10.1021/ac9809940. View

19.

Martin T, Zaugg F, Witte K, Indermuhle P, Nock S, Wagner P . Monolayers of derivatized poly(L-lysine)-grafted poly(ethylene glycol) on metal oxides as a class of biomolecular interfaces. Proc Natl Acad Sci U S A. 2001; 98(3):852-7. PMC: 14673. DOI: 10.1073/pnas.98.3.852. View

20.

Mori T, Oguro A, Ohtsu T, Nakamura Y . RNA aptamers selected against the receptor activator of NF-kappaB acquire general affinity to proteins of the tumor necrosis factor receptor family. Nucleic Acids Res. 2004; 32(20):6120-8. PMC: 534629. DOI: 10.1093/nar/gkh949. View