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Oligonucleotides Containing 7‐Deaza‐2′‐deoxyinosine as Universal Nucleoside: Synthesis of 7‐Halogenated and 7‐Alkynylated Derivatives, Ambiguous Base Pairing, and Dye Functionalization by the Alkyne–Azide ‘Click’ Reaction
Author(s) -
Seela Frank,
Ming Xin
Publication year - 2008
Publication title -
helvetica chimica acta
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.74
H-Index - 82
eISSN - 1522-2675
pISSN - 0018-019X
DOI - 10.1002/hlca.200890131
Subject(s) - chemistry , oligonucleotide , click chemistry , nucleobase , combinatorial chemistry , phosphoramidite , stereochemistry , duplex (building) , nucleic acid analogue , azide , regioselectivity , nucleic acid , dna , organic chemistry , nucleic acid thermodynamics , biochemistry , base sequence , catalysis
Abstract Oligonucleotides containing 7‐deaza‐2′‐deoxyinosine derivatives bearing 7‐halogen substituents or 7‐alkynyl groups were prepared. For this, the phosphoramidites 2b – 2g containing 7‐substituted 7‐deaza‐2′‐deoxyinosine analogues 1b – 1g were synthesized ( Scheme 2 ). Hybridization experiments with modified oligonucleotides demonstrate that all 2′‐deoxyinosine derivatives show ambiguous base pairing, as 2′‐deoxyinosine does. The duplex stability decreases in the order C d >A d >T d >G d when 2b – 2g pair with these canonical nucleosides ( Table 6 ). The self‐complementary duplexes 5′‐d(F 7 c 7 I‐C) 6 , d(Br 7 c 7 I‐C) 6 , and d(I 7 c 7 I‐C) 6 are more stable than the parent duplex d(c 7 I‐C) 6 ( Table 7 ). An oligonucleotide containing the octa‐1,7‐diyn‐1‐yl derivative 1g , i.e. , 27 , was functionalized with the nonfluorescent 3‐azido‐7‐hydroxycoumarin ( 28 ) by the Huisgen–Sharpless–Meldal cycloaddition ‘click’ reaction to afford the highly fluorescent oligonucleotide conjugate 29 ( Scheme 3 ). Consequently, oligonucleotides incorporating the derivative 1g bearing a terminal CC bond show a number of favorable properties: i ) it is possible to activate them by labeling with reporter molecules employing the ‘click’ chemistry. ii ) Space demanding residues introduced in the 7‐position of the 7‐deazapurine base does not interfere with duplex structure and stability ( Table 8 ). iii ) The ambiguous pairing character of the nucleobase makes them universal probes for numerous applications in oligonucleotide chemistry, molecular biology, and nanobiotechnology.