A Bright and Ionizable Cytosine Mimic for i-Motif Structures

A new fluorescent cytosine analog "C-ts"containing a trans-stilbene moiety was synthesizedand incorporated into hemiprotonated base pairs that comprise i-motif structures. Unlike previously reported fluorescentbase analogs, C-ts mimics the acid-base propertiesof cytosine (pK (a) & AP;...

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Bibliographic Details
Published inBioconjugate chemistry Vol. 34; no. 6; pp. 972 - 976
Main Authors Karimi, Ashkan, Wang, Kaixiang, Basran, Kaleena, Copp, William, Luedtke, Nathan W.
Format Journal Article
LanguageEnglish
Published WASHINGTON Amer Chemical Soc 17.05.2023
Subjects
Biochemical Research Methods
Biochemistry & Molecular Biology
Chemistry
Chemistry, Multidisciplinary
Chemistry, Organic
Life Sciences & Biomedicine
Physical Sciences
Science & Technology
ANALOG
DNA
GENE-EXPRESSION
NUCLEAR-PROTEIN
PROMOTER
G-QUADRUPLEX
BINDING
FLUORESCENT-PROBE
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Summary:A new fluorescent cytosine analog "C-ts"containing a trans-stilbene moiety was synthesizedand incorporated into hemiprotonated base pairs that comprise i-motif structures. Unlike previously reported fluorescentbase analogs, C-ts mimics the acid-base propertiesof cytosine (pK (a) & AP; 4.3) while exhibitingbright (& epsilon; x & phi; & AP; 1000 cm(-1) M-1) and red-shifted fluorescence (& lambda;(em) = 440 & RARR; 490 nm) upon its protonation in the water-excludedinterface of C-ts(+):C base pairs. Ratiometricanalyses of C-ts emission wavelengths facilitate real-timetracking of reversible conversions between single-stranded, double-stranded,and i-motif structures derived from the human telomericrepeat sequence. Comparisons between local changes in C-ts protonation with global structure changes according to circulardichroism suggest partial formation of hemiprotonated base pairs inthe absence of global i-motif structures at pH =6.0. In addition to providing a highly fluorescent and ionizable cytosineanalog, these results suggest that hemiprotonated C+:Cbase pairs can form in partially folded single-stranded DNA in theabsence of global i-motif structures.
ISSN:1043-1802
1520-4812
DOI:10.1021/acs.bioconjchem.3c00055