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DNA Strand Displacement with Base Pair Stabilizers: Purine‐2,6‐Diamine and 8‐Aza‐7‐Bromo‐7‐Deazapurine‐2,6‐Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction
Author(s) -
Zhang Aigui,
Kondhare Dasharath,
Leonard Peter,
Seela Frank
Publication year - 2022
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.202202412
Subject(s) - oligonucleotide , dna , nucleobase , chemistry , base pair , diamine , fluorescence , combinatorial chemistry , stereochemistry , biophysics , photochemistry , biochemistry , polymer chemistry , biology , physics , quantum mechanics
Purine‐2,6‐diamine and 8‐aza‐7‐deaza‐7‐bromopurine‐2,6‐diamine 2’‐deoxyribonucleosides ( 1 and 2 ) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA‐dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single‐stranded invaders with single and multiple incorporations of stabilizers. Displacement is driven by negative enthalpy changes between target and displaced duplex. Toeholds are not required. Two new environmental sensitive fluorescent pyrene sensors were developed to monitor the progress of displacement reactions. Pyrene was connected to the nucleobase in the invader or to a dendritic linker in the output strand. Both new sensors were constructed by click chemistry; phosphoramidites and oligonucleotides were prepared. Sensors show monomer or excimer emission. Fluorescence intensity changes when the displacement reaction progresses. Our work demonstrates that strand displacement with base pair stabilizers is applicable to DNA, RNA and to related biopolymers with applications in chemical biology, nanotechnology and medicinal diagnostics.