title: Tuning the pH Response of i-Motif DNA Oligonucleotides.
abstract: Cytosine-rich single-stranded DNA oligonucleotides are able to adopt an i-motif conformation, a four-stranded structure, near a pH of 6. This unique pH-dependent conformational switch is reversible and hence can be controlled by changing the pH. Here, we show that the pH response range of the human telomeric i-motif can be shifted towards more basic pH values by introducing 5-methylcytidines (5-MeC) and towards more acidic pH values by introducing 5-bromocytidines (5-BrC). No thermal destabilisation was observed in these chemically modified i-motif sequences. The time required to attain the new conformation in response to sudden pH changes was slow for all investigated sequences but was found to be ten times faster in the 5-BrC derivative of the i-motif.
authors.affiliation: Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main (Germany).
authors.forename: Laurie
authors.initials: L
authors.lastname: Lannes
authors.affiliation: National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065 (India).
authors.forename: Saheli
authors.initials: S
authors.lastname: Halder
authors.affiliation: National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065 (India).|Department of Chemistry, University of Chicago, E305, GCIS, 929 E, 57th Street, Chicago, IL 60637 (USA).
authors.forename: Yamuna
authors.initials: Y
authors.lastname: Krishnan
authors.affiliation: Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/Main (Germany). schwalbe@nmr.uni-frankfurt.de.
authors.forename: Harald
authors.initials: H
authors.lastname: Schwalbe
mesh_terms: D044503:5-Methylcytosine / Q000737:chemistry; D001483:Base Sequence; D003596:Cytosine / Q000031:analogs & derivatives / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D059372:Nucleotide Motifs; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000235:genetics; D016615:Telomere / Q000235:genetics; D013696:Temperature
chemical_list: D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides; C103182:5-bromocytosine; D044503:5-Methylcytosine; D003596:Cytosine
keywords: bromocytidine; cytosine-rich DNA; i-motifs; methylcytidine; nanodevices; pH sensors; telomeric DNA