Jürg Hunziker

2'-Ethynyl-DNA: Synthesis and pairing properties

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.

DNA with artificial base pairs

The introduction of a single base pair with the electronically complementary base surrogates phenyl- (P) and pentafluorophenyl-deoxyriboside (F 5 ) into DNA oligonucleotides leads to a strong decrease in duplex stability. Longer stretches with alternating P-F 5 pairs can lead to duplexes with increased stability as compared to their counterparts with natural A-T base pairs. Optimization of the steric and electronic properties of the P-F 5 pair by replacing the phenyl residue with naphthalene, anisole or thioanisole leads to an increase in stability. Complementary charge distribution thus represents a novel design principle for artificial DNA base pairs. These results also highlight the importance of favorable intrastrand stacking interactions in the thermodynamic stabilization of oligonucleotide duplexes. A combination with favorable interstrand stacking could lead to a set of orthogonal, non-hydrogen bonded base pairs. Such artificial pairing systems could be used in many ways. By gradually changing the composition of linearly stacked artificial bases interesting electronic, photophysical and magnetic properties could result. The quasi one-dimensional arrangement of charge transfer complexes might pave the way for applications of the nucleic acid scaffold in material science.

Recognition of a G-C base pair by α-N7-deoxyinosine within the pyrimidine-purine-pyrimidine DNA triple helical motif

Abstract The α-nucleoside 7-(2′-deoxy-α-D-ribofuranosyl)hypoxanthine, incorporated into an otherwise β-configured oligodeoxynucleotide that is designed to bind to a DNA duplex in the parallel motif, recognizes selectively and efficiently a G-C base pair, presumably via monodentate α-H 7 ·G-C base-triple formation.

Towards a DNA-Like Duplex Without Hydrogen Bonds

Abstract The inverse quadrupolar moments of the phenyl and pentafluorophenyl residues in the base pair P-F5 promotes strong intramolecular stacking interactions in DNA duplexes. The more natural base pairs are replaced by this novel pair the higher the thermodynamic stability of the resulting duplex if they are arranged in an alternating fashion.