Otto C, Thomas G A, Rippe K, Jovin T M, Peticolas W L
Department of Chemistry, University of Oregon, Eugene 97403.
Biochemistry. 1991 Mar 26;30(12):3062-9. doi: 10.1021/bi00226a012.
Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5'-d-[(A)10TAATTTTAAATATTT]-3' (D1) and 5'-d[(T)10ATTAAAATTTATAAA]-3' (D2) in H2O and D2O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the deoxyoligonucleotides D1 and 5'-d(AAATATTTAAAATTA-(T)10]-3' (D3). The Raman spectra of the antiparallel-stranded (aps) duplex are reminiscent of the spectra of poly[d(A)].poly[d(T)] and a B-form structure similar to that adopted by the homopolymer duplex is assigned to the antiparallel double helix. The spectra of the parallel-stranded (ps) and antiparallel-stranded duplexes differ significantly due to changes in helical organization, i.e., base pairing, base stacking, and backbone conformation. Large changes observed in the carbonyl stretching region (1600-1700 cm-1) implicate the involvement of the C(2) carbonyl of thymine in base pairing. The interaction of adenine with the C(2) carbonyl of thymine is consistent wtih formation of reverse Watson-Crick base pairing in parallel-stranded DNA. Phosphate-furanose vibrations similar to those observed for B-form DNA of heterogenous sequence and high A,T content are observed at 843 and 1092 cm-1 in the spectra of the parallel-stranded duplex. The 843-cm-1 band is due to the presence of a sizable population of furanose rings in the C2'-endo conformation. Significant changes observed in the regions from 1150 to 1250 cm-1 and from 1340 to 1400 cm-1 in the spectra of the parallel-stranded duplex are attributed to variations in backbone torsional and glycosidic angles and base stacking.
已获取由脱氧寡核苷酸5'-d-[(A)10TAATTTTAAATATTT]-3'（D1）和5'-d[(T)10ATTAAAATTTATAAA]-3'（D2）在H2O和D2O中形成的平行链双链体的拉曼光谱。然后将平行链DNA的光谱与由脱氧寡核苷酸D1和5'-d(AAATATTTAAAATTA-(T)10]-3'（D3）形成的反平行双螺旋的光谱进行比较。反平行链（aps）双链体的拉曼光谱让人联想到聚[d(A)]·聚[d(T)]的光谱，并且将类似于均聚物双链体所采用的B型结构赋予反平行双螺旋。由于螺旋结构的变化，即碱基配对、碱基堆积和主链构象的变化，平行链（ps）和反平行链双链体的光谱有显著差异。在羰基伸缩区域（1600 - 1700 cm-1）观察到的大变化表明胸腺嘧啶的C(2)羰基参与了碱基配对。腺嘌呤与胸腺嘧啶的C(2)羰基的相互作用与平行链DNA中反向沃森-克里克碱基配对的形成一致。在平行链双链体的光谱中，在843和1092 cm-1处观察到与具有高A、T含量的异源序列B型DNA相似的磷酸-呋喃糖振动。843-cm-1处的谱带归因于相当数量的呋喃糖环处于C2'-内型构象。在平行链双链体的光谱中，在1150至1250 cm-1区域和1340至1400 cm-1区域观察到的显著变化归因于主链扭转角和糖苷键角以及碱基堆积的变化。
