i-Clamp phenoxazine for the fine tuning of DNA i-motif stability

Nucleic Acids Research
Vladimir B TsvetkovAndrey V Aralov

Abstract

Non-canonical DNA structures are widely used for regulation of gene expression, in DNA nanotechnology and for the development of new DNA-based sensors. I-motifs (iMs) are two intercalated parallel duplexes that are held together by hemiprotonated C-C base pairs. Previously, iMs were used as an accurate sensor for intracellular pH measurements. However, iM stability is moderate, which in turn limits its in vivo applications. Here, we report the rational design of a new substituted phenoxazine 2'-deoxynucleotide (i-clamp) for iM stabilization. This residue contains a C8-aminopropyl tether that interacts with the phosphate group within the neighboring chain without compromising base pairing. We studied the influence of i-clamp on pH-dependent stability for intra- and intermolecular iM structures and found the optimal positions for modification. Two i-clamps on opposite strands provide thermal stabilization up to 10-11°C at a pH of 5.8. Thus, we developed a new modification that shows significant iM-stabilizing effect both at strongly and mildly acidic pH and increases iM transition pH values. i-Clamp can be used for tuning iM-based pH probes or assembling extra stable iM structures for various applications.

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Citations

Jun 8, 2018·Chemical Communications : Chem Comm·Sagar SatpathiPartha Hazra
Jan 3, 2019·Angewandte Chemie·Manish DebnathJyotirmayee Dash
Jul 3, 2019·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Isabell SchönrathJens Müller
Jul 29, 2020·Organic & Biomolecular Chemistry·Vladimir B TsvetkovAndrey V Aralov
Aug 21, 2018·Nucleic Acids Research·Hala Abou AssiMasad J Damha
Aug 7, 2020·Organic & Biomolecular Chemistry·Alexandre DevauxEric Defrancq
Feb 23, 2020·Frontiers in Chemistry·Mahmoud A S Abdelhamid, Zoë A E Waller
Dec 3, 2020·Nucleic Acids Research·Prakash KharelPavel Ivanov
Dec 15, 2020·Biosensors & Bioelectronics·Anton V TuraevAnna M Varizhuk
Mar 2, 2021·Chemical Society Reviews·Luke K McKenzieMarcel Hollenstein
Apr 21, 2021·Journal of Inorganic Biochemistry·Isabell SchönrathJens Müller
Jan 4, 2019·Chemical Reviews·Jean-Louis Mergny, Dipankar Sen
Jan 27, 2019·Antiviral Research·Liubov I KozlovskayaAndrey V Aralov

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Methods Mentioned

BETA
NMR
chemical
electrophoresis
circular dichroism
electrophoretic mobility assay

Software Mentioned

Clamp
VMD
Promass
Sybyl
Gaussian
Amber
DataFit

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