title: Rationally designing aptamer sequences with reduced affinity for controlled sensor performance.
abstract: The relative ease of predicting the secondary structure of nucleic acid sequences lends itself to the design of sequences to perform desired functions. Here, we combine the utility of nucleic acid aptamers with predictable control over the secondary structure to rationally design sequences with controlled affinity towards a target analyte when employed as the recognition element in an electrochemical sensor. Specifically, we present a method to modify an existing high-gain aptamer sequence to create sequences that, when employed in an electrochemical, aptamer-based sensor, exhibit reduced affinity towards a small molecule analyte tobramycin. Sensors fabricated with the high-gain parent sequence saturate at concentrations much below the therapeutic window for tobramycin (7-18 µM). Accordingly, the rationale behind modifying this high-gain sequence to reduce binding affinity was to tune sensor performance for optimal sensitivity in the therapeutic window. Using secondary structure predictions and analysis of the NMR structure of an aminoglycoside RNA aptamer bound to tobramycin, we are able to successfully modify the aptamer sequence to tune the dissociation constants of electrochemical aptamer-based sensors between 0.17 and 3 µM. The guidelines we present represent a general strategy to lessening binding affinity of sensors employing aptamer-modified electrodes.
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA. SLaur1@umbc.edu.
authors.forename: Lauren R
authors.initials: LR
authors.lastname: Schoukroun-Barnes
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA. rjwhite@umbc.edu.
authors.forename: Ryan J
authors.initials: RJ
authors.lastname: White
mesh_terms: D000617:Aminoglycosides / Q000737:chemistry; D000818:Animals; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D004563:Electrochemistry; D006801:Humans
chemical_list: D000617:Aminoglycosides; D052157:Aptamers, Nucleotide
references.citation: Nat Struct Biol. 1998 Sep;5(9):769-74
references.pmid: 9731769
references.citation: Analyst. 2015 Jun 7;140(11):3794-802
references.pmid: 25620243
references.citation: Nanotechnology. 2011 Sep 2;22(35):355502
references.pmid: 21828892
references.citation: Anal Chem. 2010 Sep 1;82(17):7090-5
references.pmid: 20687587
references.citation: RNA. 1998 Jun;4(6):669-79
references.pmid: 9622126
references.citation: Chem Rev. 2000 Jul 12;100(7):2693-704
references.pmid: 11749301
references.citation: Anal Chem. 2014 Nov 18;86(22):11417-24
references.pmid: 25337781
references.citation: J Am Chem Soc. 2008 Apr 2;130(13):4256-8
references.pmid: 18324816
references.citation: Anal Chem. 2014 Jan 21;86(2):1131-7
references.pmid: 24377296
references.citation: Biotechnol Prog. 2000 Jul-Aug;16(4):610-6
references.pmid: 10933836
references.citation: Anal Chem. 2013 Jan 2;85(1):121-8
references.pmid: 23210972
references.citation: Colloids Surf B Biointerfaces. 2011 Jan 1;82(1):168-72
references.pmid: 20843666
references.citation: Biophys Chem. 2002 May 2;96(2-3):213-28
references.pmid: 12034442
references.citation: Anal Chem. 2009 Nov 1;81(21):9109-13
references.pmid: 19810694
references.citation: Angew Chem Int Ed Engl. 2012 Jul 2;51(27):6717-21
references.pmid: 22674785
references.citation: Chem Soc Rev. 2010 May;39(5):1747-63
references.pmid: 20419217
references.citation: J Am Chem Soc. 2011 Jun 15;133(23):8862-5
references.pmid: 21574588
references.citation: Chem Biol. 1995 May;2(5):281-90
references.pmid: 9383430
references.citation: Langmuir. 2008 Sep 16;24(18):10513-8
references.pmid: 18690727
references.citation: Anal Chem. 2012 Jan 17;84(2):685-707
references.pmid: 22044045
references.citation: Angew Chem Int Ed Engl. 2003 Oct 20;42(40):4872-97
references.pmid: 14579432
references.citation: Angew Chem Int Ed Engl. 2006 Feb 13;45(8):1190-6
references.pmid: 16432908
references.citation: Curr Opin Chem Biol. 2012 Aug;16(3-4):422-8
references.pmid: 22503680
references.citation: Analyst. 2010 Mar;135(3):589-94
references.pmid: 20174715
references.citation: Langmuir. 2009 Apr 21;25(8):4279-83
references.pmid: 19301828
references.citation: Bioelectrochemistry. 2009 Sep;76(1-2):208-13
references.pmid: 19362061
references.citation: J Am Chem Soc. 2009 Apr 1;131(12):4262-6
references.pmid: 19271708
references.citation: Proc SPIE Int Soc Opt Eng. 2009;7321:732105
references.pmid: 20436792
references.citation: J Am Chem Soc. 2012 Feb 15;134(6):2876-9
references.pmid: 22239688
references.citation: Enzyme Microb Technol. 2011 Feb 8;48(2):107-22
references.pmid: 22112819
references.citation: Langmuir. 2007 Jun 5;23(12):6827-34
references.pmid: 17488132
references.citation: J Infect Dis. 1976 Aug;134 Suppl:S125-9
references.pmid: 972270
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references.pmid: 12824337
references.citation: Anal Chem. 2010 Jan 1;82(1):73-6
references.pmid: 20000457
references.citation: J Am Chem Soc. 2010 Nov 17;132(45):16120-6
references.pmid: 20964337