Synthesis of 2′‐Deoxyoxanosine from 2′‐Deoxyguanosine, Conversion to Its Phosphoramidite, and Incorporation into Oxanine‐Containing Oligodeoxynucleotides

Pack, Seung Pil; Makino, Keisuke

doi:10.1002/0471142700.nc0439s41

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“…However, there has not been as of yet consensus on its structure, because structural studies on DNA oligomers containing the O:C mismatch have not been carried out by NMR or X-ray crystallography so far on account of difficulties in preparing a dOxa amidite monomer. Since the monomer has been successfully synthesized and employed to the automatic DNA synthesizer ( 13 , 16 ), it has become possible to investigate how the mismatch of Oxa base pair affects the structure and properties of the Oxa duplexes at an atomic resolution. Recently, biotechnological utilization of the dOxa oligonucleotides has been reported.…”

Section: Introductionmentioning

confidence: 99%

Solution structure and stability of the DNA undecamer duplexes containing oxanine mismatch

Pack

Morimoto

Makino

et al. 2011

Nucleic Acids Research

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Solution structures of DNA duplexes containing oxanine (Oxa, O) opposite a cytosine (O:C duplex) and opposite a thymine (O:T duplex) have been solved by the combined use of 1H NMR and restrained molecular dynamics calculation. One mismatch pair was introduced into the center of the 11-mer duplex of [d(GTGACO6CACTG)/d(CAGTGX17GTCAC), X = C or T]. 1H NMR chemical shifts and nuclear Overhauser enhancement (NOE) intensities indicate that both the duplexes adopt an overall right-handed B-type conformation. Exchangeable resonances of C17 4-amino proton of the O:C duplex and of T17 imino proton of O:T duplex showed unusual chemical shifts, and disappeared with temperature increasing up to 30°C, although the melting temperatures were >50°C. The O:C mismatch takes a wobble geometry with positive shear parameter where the Oxa ring shifted toward the major groove and the paired C17 toward the minor groove, while, in the O:T mismatch pair with the negative shear, the Oxa ring slightly shifted toward the minor groove and the paired T17 toward the major groove. The Oxa mismatch pairs can be wobbled largely because of no hydrogen bond to the O1 position of the Oxa base, and may occupy positions in the strands that optimize the stacking with adjacent bases.

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Section: Introductionmentioning

confidence: 99%