Marotta S P, Sheardy R D
Department of Chemistry, Seton Hall University, South Orange, New Jersey 07079, USA.
Biophys J. 1996 Dec;71(6):3361-9. doi: 10.1016/S0006-3495(96)79529-2.
Three sets of semi-self-complementary deoxyribonucleotide decamers with the sequence XX-(5meCG)4, (5meCG)4-XX, or Y-(5meCG)4-Y, where XX = AA, CC, GG, or TT and Y = A, C, G, or T, were synthesized along with the self-complementary octamer (5meCG)4. The 8-mer duplex readily undergoes a B-to-Z conformational conversion upon increasing the NaCl concentration with a transitional midpoint of approximately 1.1 M NaCl. The 10-mers should form 8-bp duplexes a with core sequence of [(5meCG)4]2 with 5'-XX overhangs, 3'-XX overhangs, or 5',3'-Y/Y mismatches. Circular dichroism was employed to determine the conformations of all oligomers. Salt titrations were performed to measure the effect of overhangs and terminal mismatches on the B-to-Z conversion. In general, the presence of 5'-XX overhangs results in a transition midpoint equal to or slightly higher than the control, whereas the presence of 3'-XX overhangs results in a transition midpoint slightly lower than the control. The 3'-CC and 5'-GG overhangs are exceptions, with transition midpoints much higher than the control. These oligomers apparently form duplexes with 5',3'-C/C or 5',3'-G/G mismatches abutting a [(G5meC)4]2 duplex core. The presence of terminal mismatches in the third set of oligomers results in transition midpoints higher than the control. Ultraviolet absorbance methods were used to evaluate the effect of the various stacking motifs of the 10-mers on the thermodynamics of melting relative to the 8-mer for both B and Z conformations. We found that in both the B and Z conformations, the presence of an overhang stabilizes the [(5meCG)4]2 duplex, with the 5' overhangs having a greater stabilizing effect relative to the 3' overhangs. The presence of 5',3'-Y/Y mismatches also imparts a stabilizing effect on the control 8-mer in both the B and Z conformations. These results are discussed in terms of stacking interactions of the terminal unpaired bases.
合成了三组半自互补脱氧核糖核苷酸十聚体，其序列分别为XX-(5meCG)4、(5meCG)4-XX或Y-(5meCG)4-Y，其中XX = AA、CC、GG或TT，Y = A、C、G或T，同时还合成了自互补八聚体(5meCG)4。随着NaCl浓度增加，该8聚体双链体很容易发生从B构象到Z构象的转变，转变中点约为1.1 M NaCl。这些十聚体应形成核心序列为[(5meCG)4]2的8碱基对双链体，带有5'-XX突出端、3'-XX突出端或5',3'-Y/Y错配。采用圆二色性来确定所有寡聚物的构象。进行盐滴定以测量突出端和末端错配对B-Z转变的影响。一般来说，5'-XX突出端的存在导致转变中点等于或略高于对照，而3'-XX突出端的存在导致转变中点略低于对照。3'-CC和5'-GG突出端是例外，其转变中点远高于对照。这些寡聚物显然形成了双链体，其中5',3'-C/C或5',3'-G/G错配邻接[(G5meC)4]2双链体核心。第三组寡聚物中末端错配的存在导致转变中点高于对照。采用紫外吸收法评估十聚体的各种堆积基序对B和Z构象相对于8聚体的熔解热力学的影响。我们发现，在B和Z构象中，突出端的存在都能稳定[(5meCG)4]2双链体，5'突出端相对于3'突出端具有更大的稳定作用。5',3'-Y/Y错配的存在在B和Z构象中也对对照8聚体具有稳定作用。根据末端未配对碱基的堆积相互作用对这些结果进行了讨论。
