A direct assignment of all base anomeric H1′ signals in the proton spectrum of a trinucleoside diphosphate, ApApA: Structure implications

Trinucleotides can be considered as primitive models for triplet codons of t-RNA and there is accordingly considerable interest in defining structures and conformations for these molecules. An important step in this direction was made recently [ I] with the first successful crystal structure determination for a trinucleoside dephosphate, adenylyl-(3’-5’)-adenylyl(3’-5’)-adenosine, ApAp?A’. Because it is difficult to predict what effect solution forces will have on structure, particularly for smaller molecules with conformational flexibility, it is essential to obtain comparable structural information in solution. However, the use of NMR spectroscopy for this purpose is severely restricted because of extensive signal overlap, especially in homo-oligonucleotides, i.e. XpXpX. Selective labeling of nucleotidyl units [2,3] is an obvious solution to overlap problems and in this communication we describe the use of this approach to achieve the first direct assignment of base and anomeric Hl’ protons for a homo-oligonucleotide, ApApA.