posted on 2015-10-29, 00:00authored byDorith Wunnicke, Ping Ding, Haozhe Yang, Frank Seela, Heinz-Jürgen Steinhoff
Parallel-stranded (ps) DNA characterized
by its sugar–phosphate
backbones pointing in the same direction represents an alternative
pairing system to antiparallel-stranded (aps) DNA with the potential
to inhibit transcription and translation. 25-mer oligonucleotides
were selected containing only dA·dT base pairs to compare spin-labeled
nucleobase distances over a range of 10 or 15 base pairs in ps DNA
with those in aps DNA. By means of the copper(I)-catalyzed Huisgen–Meldal–Sharpless
alkyne–azide cycloaddition, the spin label 4-azido-2,2,6,6-tetramethylpiperidine-1-oxyl
was clicked to 7-ethynyl-7-deaza-2′-deoxyadenosine or 5-ethynyl-2′-deoxyuridine
to yield 25-mer oligonucleotides incorporating two spin labels. The
interspin distances between spin labeled residues were determined
by pulse EPR spectroscopy. The results reveal that in ps DNA these
distances are between 5 and 10% longer than in aps DNA when the labeled
DNA segment is located near the center of the double helix. The interspin
distance in ps DNA becomes shorter compared with aps DNA when one
of the spin labels occupies a position near the end of the double
helix.