A universal, photocleavable DNA base: nitropiperonyl 2'-deoxyriboside.
A universal, photochemically cleavable DNA base analogue would add desirable versatility to a number of methods in molecular biology. A novel C-nucleoside, nitropiperonyl deoxyriboside (NPdR, P), has been investigated for this purpose. NPdR can be converted to its 5'-DMTr-3'-CE-phosphoramidite and was incorporated into pentacosanucleotides by conventional synthesis techniques. The destabilizing effect on hybrid formation with a complementary strand when this P base opposes A, T, and G was found to be 3-5 kcal/mol, but 9 kcal/mol when it opposes C. Brief irradiation (lambda > 360 nm, 20 min) of DNA containing the P base and piperidine treatment causes strand cleavage giving the 3'- and 5'-phosphates. Two significant recent interests, universal/non-hydrogen-bonding base analogues and photochemical backbone cleavage, have thus been combined in a single molecule that serves as a light-based DNA scissors.
Pirrung
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MC
Department of Chemistry, Levine Science Research Center, Duke University, Durham, North Carolina 27708-0317, USA. pirrung@chem.duke.edu
Zhao
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X
Harris
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D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D006868:Hydrolysis; D019906:Nuclear Magnetic Resonance, Biomolecular; D009693:Nucleic Acid Hybridization; D009705:Nucleosides / Q000737:chemistry*; D010777:Photochemistry; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013816:Thermodynamics
D009705:Nucleosides; C427479:nitropiperonyl 2'-deoxyriboside; D004247:DNA