2′-Ethynyl-DNA: Synthesis and Pairing Properties

Abstract

2-Ethynyl-DNA was developed as a potential DNA-selective oligonucleotide analog. The synthesis of 2′-arabino-ethynyl-modified nucleosides was achieved starting from properly protected 2′-ketonucleosides by addition of lithium (trimethylsilyl)acetylide followed by reduction of the tertiary alcohol. After a series of protecting-group manipulations, phosphoramidite building blocks suitable for solid-phase synthesis were obtained. The synthesis of oligonucleotides from these building blocks was successful when a fast deprotection scheme was used. The pairing properties of 2′-arabino-ethynyl-modified oligonucleotides can be summarized as follows: 1) The 2′-arabino-ethynyl modification of pyrimidine nucleosides leads to a strong destabilization in duplexes with DNA as well as with RNA. The likely reason is that the ethynyl group sterically influences the torsional preferences around the glycosidic bond leading to a conformation not suitable for duplex formation. 2) If the modification is introduced in purine nucleosides, no such influence is observed. The pairing properties are not or only slightly changed, and, in some cases (deoxyadenosine homo-polymers), the desired stabilization of the pairing with a DNA complementary strand and destabilization with an RNA complement is observed. 3) In oligonucleotides of alternating deoxycytidine-deoxyguanosine sequence, the incorporation of 2′-arabino-ethynyl deoxyguanosine surprisingly leads to the formation of a left-handed double helix, irrespective of salt concentration. The rationalization for this behavior is that the ethynyl group locks such duplexes in a left-handed conformation through steric blockade.