Nucleic acids play essential roles in gene storage and expression, show catalytic activity and function as regulatory elements. The majority of these numerous functions rely on the nucleic acid’s ability to fold into complex three-dimensional structures and in many cases the dynamic contribution might be the key to understanding and manipulating their activity. Continuous wave (CW) and pulsed electron paramagnetic resonance (EPR) spectroscopy have emerged as powerful tools for studying structure and dynamics of nucleic acids by providing information on local environments or distances between EPR active components.
Due to the diamagnetic nature of natural nucleic acids, EPR experiments depend on introduction of spin labels. A number of spin labels is known, however, most of them are linked to the macromolecule via flexible tethers, which results in poorer resolution and broader distance distributions in EPR measurements. These disadvantages can be overcome by using rigid spin labels in which the rotation along connecting molecular bonds in hindered. However, up to now, available rigid spin labels were limited to deoxycytidine or 2’-O-Me-cytidine.
Here, the synthesis of two novel rigid adenosine-derived spin labels suitable for introduction into DNA and RNA oligonucleotides is presented. The successful design of both spin labels is underlined by thermal melting profiles of labeled oligonucleotides and first EPR measurements.