Polarity of Major Grooves Explored by Using an Isosteric Emissive Nucleoside

Abstract

Feelin' groovy: An emissive furan‐containing nucleoside, which serves as a minimally invasive isomorphic thymine analogue, was used to estimate groove polarity in DNA. By determining the associated microscopic solvent‐polarity value ET(30) as shown in the figure, a rather apolar environment was detected. Such studies are likely to shed new light on fundamentally important questions regarding biopolymeric microenvironments.

Synthesis and spectral characterization of environmentally responsive fluorescent deoxycytidine analogs

“…24 Overall, we report the synthesis and spectral characterization of five pyrrolocytidine deoxynucleosides and a C5-ethynyl derivative of deoxycytidine (2b) and of deoxyuridine (2a). In particular, we have examined the effects of solvent polarity 25 and solvent viscosity 26 on the fluorescence associated these analogs.…”

Fluorescent Nucleic Acid Analogues in Research and Clinical Diagnostics

“…For B-type helix, a wide and broad major groove and a smaller minor groove are distinguished (Baraldi et al 2004;Rohs et al 2009). Polarity of the grooves and accessibility to nucleobases are also different (Sinkeldam et al 2008). Positioning of fluorophore within the grooves can be achieved non-covalently (e.g., BOXTO dye) (Strekowski and Wilson 2007;Astakhova et al 2013a, b) or by covalent internal attachment of the label to the sugar or nucleobase via a relatively short linker (Kumar et al 2006(Kumar et al , 2007a(Kumar et al , b, 2009Kolb et al 2001;Sletten and Bertozzi 2009;Lallana et al 2011;Grammel and Hang 2013;Xie et al 2013).…”

Nucleotides and Nucleic Acids; Oligo- and Polynucleotides

“…193 The effect of solvent polarity in the major groove of duplex DNA has been examined using 5-furano-dU, which is emissive and sensitive to its microenvironment. 194 A large number of publications have use C5-alkynylated pyrimidine analogues for Click chemistry. 5-Ethynyluracil has been used for Click chemistry with an azidofluorophore to detect DNA 195 and RNA 196 synthesis in vivo for the detection of cells in S-phase as an alternative to 5-bromo-dU antibodies.…”