DNA with Parallel Strand Orientation: A Nanometer Distance Study with Spin Labels in the Watson-Crick and the Reverse Watson-Crick Double Helix

Autor(en): Wunnicke, Dorith
Ding, Ping
Yang, Haozhe
Seela, Frank
Steinhoff, Heinz-Juergen 
Stichwörter: CHAIN ORIENTATION; Chemistry; Chemistry, Physical; DUPLEX DNA; EPR SPECTROSCOPY; FORCE-FIELD; NMR STRUCTURE; NUCLEIC-ACIDS; OLIGONUCLEOTIDE DUPLEXES; SEQUENCE; TRANSITION; TRIPLEX DNA
Erscheinungsdatum: 2015
Herausgeber: AMER CHEMICAL SOC
Journal: JOURNAL OF PHYSICAL CHEMISTRY B
Volumen: 119
Ausgabe: 43
Startseite: 13593
Seitenende: 13599
Zusammenfassung: 
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.
ISSN: 15206106
DOI: 10.1021/acs.jpcb.5b02935

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