Optimization of SELEX: Comparison of different methods for monitoring the progress of in vitro selection of aptamers

Journal of Pharmaceutical and Biomedical Analysis

Volumn 91, Issue , 2014, Pages 151-159

  Mencin, Nina ^a,b   Šmuc, Tina ^b   Vraničar, Marko ^b   Mavri, Jan ^b   Hren, Matjaž ^b   Galeša, Katja ^b   Krkoč, Peter ^b   Ulrich, Henning ^c   Šolar, Borut ^b  

^a Instrumentation Technologies   (Slovenia)

^b Centre of Excellence for Biosensors   (Slovenia)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Aptamer; Aptamer pool evolution; Evolution monitoring; Selection progress; SELEX

Indexed keywords

APTAMER; DNA; STREPTAVIDIN;

ARTICLE; BINDING AFFINITY; BINDING ASSAY; COMBINATORIAL CHEMISTRY; DISSOCIATION CONSTANT; FLUORESCENCE ANALYSIS; FOLLOW UP; GENE SEQUENCE; IN VITRO SELECTION; INTERMETHOD COMPARISON; MELTING CURVE ANALYSIS; MELTING POINT; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; PROCESS OPTIMIZATION; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RESTRICTION SITE; SEQUENCE ANALYSIS; STEADY STATE;

APTAMER; APTAMER POOL EVOLUTION; EVOLUTION MONITORING; SELECTION PROGRESS; SELEX;

APTAMERS, NUCLEOTIDE; OLIGONUCLEOTIDES; SELEX APTAMER TECHNIQUE; STREPTAVIDIN;

EID: 84892880864     PISSN: 07317085     EISSN: 1873264X     Source Type: Journal    
DOI: 10.1016/j.jpba.2013.12.031     Document Type: Article

References (25)

1. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249(August (4968)):505-510.
2. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346(August (6287)):818-822.
3. Mann D., Reinemann C., Stoltenburg R., Strehlitz B. In vitro selection of DNA aptamers binding ethanolamine. Biochem. Biophys. Res. Commun. 2005, 338(December (4)):1928-1934.
4. Hofmann H.P., Limmer S., Hornung V., Sprinzl M. Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair. RNA 1997, 3(November (11)):1289-1300.
5. Yang Q., Goldstein I.J., Mei H.Y., Engelke D.R. DNA ligands that bind tightly and selectively to cellobiose. Proc. Natl. Acad. Sci. U.S.A. 1998, 95(May (10)):5462-5467.
6. Jellinek D., Green L.S., Bell C., Janjić N. Inhibition of receptor binding by high-affinity RNA ligands to vascular endothelial growth factor. Chemistry 1994, 33(August (34)):10450-10456.
7. Bock L.C., Griffin L.C., Latham J.A., Vermaas E.H., Toole J.J. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 1992, 355(February (6360)):564-566.
8. Ulrich H., Magdesian M.H., Alves M.J., Colli W. In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion. J. Biol. Chem. 2002, 277(June (23)):20756-20762.
9. Šmuc T., Ahn I.Y., Ulrich H. Nucleic acid aptamers as high affinity ligands in biotechnology and biosensorics. J. Pharm. Biomed. Anal. 2013, 81-82:210-217.
10. Vant-Hull B., Payano-Baez A., Davis R.H., Gold L. The mathematics of SELEX against complex targets. J. Mol. Biol. 1998, 278(May (3)):579-597.
11. Irvine D., Tuerk C., Gold L. SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis. J. Mol. Biol. 1991, 222(December (3)):739-761.
12. Stoltenburg R., Reinemann C., Strehlitz B. FluMag-SELEX as an advantageous method for DNA aptamer selection. Anal. Bioanal. Chem. 2005, 383(September (1)):83-91.
13. Bing T., Yang X., Mei H., Cao Z., Shangguan D. Conservative secondary structure motif of streptavidin-binding aptamers generated by different laboratories. Bioorg. Med. Chem. 2010, 18(March (5)):1798-1805.
14. Qian J., Lou X., Zhang Y., Xiao Y., Soh H.T. Generation of highly specific aptamers via micromagnetic selection. Anal. Chem. 2009, 81(May (13)):5490-5495.
15. Stoltenburg R., Reinemann C., Strehlitz B. SELEX-A. (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol. Eng. 2007, 24(October (4)):381-403.
16. Musheev M.U., Krylov S.N. Selection of aptamers by systematic evolution of ligands by exponential enrichment: addressing the polymerase chain reaction issue. Anal. Chim. Acta 2006, 564(March (1)):91-96.
17. Pestourie C., Cerchia L., Gombert K., Aissouni Y., Boulay J., De Franciscis V., Libri D., Tavitian B., Ducongé F. Comparison of different strategies to select aptamers against a transmembrane protein target. Oligonucleotides 2006, 16(Winter (4)):323-335.
18. Schütze T., Arndt P.F., Menger M., Wochner A., Vingron M., Erdmann V.A., Lehrach H., Kaps C., Glökler J. A calibrated diversity assay for nucleic acid libraries using DiStRO-a diversity standard of random oligonucleotides. Nucleic Acids Res. 2010, 38(March (4)):e23.
19. Charlton J., Smith D. Estimation of SELEX pool size by measurement of DNA renaturation rates. RNA 1999, 5(October (10)):1326-1332.
20. Markham N.R., Zuker M. UNAFold Software for nucleic acid folding and hybridization. Methods Mol. Biol. 2008, 453:3-31.
21. Avci-Adali M., Wilhelm N., Perle N., Stoll H., Schlensak C., Wendel H.P. Absolute quantification of cell-bound DNA aptamers during SELEX. Nucleic Acid Ther. 2013, 23(April (2)):125-130.
22. Colborn J.M., Byrd B.D., Koita O.A., Krogstad D.J. Estimation of copy number using SYBR green: confounding by AT-rich DNA and by variation in amplicon length. Am. J. Trop. Med. Hyg. 2008, 79(December (6)):887-892.
23. Shi H., Fan X., Ni Z., Lis J.T. Evolutionary dynamics and population control during in vitro selection and amplification with multiple targets. RNA 2002, 8(November (11)):1461-1470.
24. Müller J., El-Maarri O., Oldenburg J., Pötzsch B., Mayer G. Monitoring the progression of the in vitro selection of nucleic acid aptamers by denaturing high-performance liquid chromatography. Anal. Bioanal. Chem. 2008, 390(February (4)):1033-1037.
25. Jing M., Bowser M.T. Methods for measuring aptamer-protein equilibria: a review. Anal. Chim. Acta 2011, 686(February (1-2)):9-18.