Robinson H, Wang A H
Biophysics Division, University of Illinois, Urbana-Champaign 61801.
Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5224-8. doi: 10.1073/pnas.90.11.5224.
The structure of the non-self-complementary DNA heptamer d(CGACGAC) at low pH has been determined by the quantitative NMR refinement procedure designated SPEDREF (SPEctral-Driven REFinement). Acid-base titration of the molecule indicated a prominent n = 2 pKa near 6.8. In the pH range up to 6.0, the heptamer forms a remarkably stable double helix, which was conclusively shown to be an unusual homobase-paired parallel-stranded double helix (termed II-DNA). In this II-DNA helix, the 5'-CGA trinucleotide is the structural motif that accounts for the stability, with the C+-C hemiprotonated base pair (in which C+ is N3-protonated cytosine) providing for the alignment site and the unusual interstrand G-A base stack in the GpA step furnishing the additional stabilizing forces. The exchangeable proton data from two-dimensional nuclear Overhauser effect spectroscopy are in total agreement with the refined structure. We conclude that the 5'-CGA or other related sequences (e.g., 5'-CCGA) are powerful motifs in promoting the II-DNA or II-RNA conformations that may play certain biological functions.
通过名为SPEDREF(光谱驱动精炼)的定量核磁共振精炼程序,已确定了低pH值下非自互补DNA七聚体d(CGACGAC)的结构。该分子的酸碱滴定表明,在6.8附近有一个显著的n = 2 pKa。在pH值高达6.0的范围内,七聚体形成了一个非常稳定的双螺旋结构,最终证明这是一种不寻常的同碱基配对平行链双螺旋结构(称为II-DNA)。在这种II-DNA螺旋中,5'-CGA三核苷酸是决定稳定性的结构基序,C⁺-C半质子化碱基对(其中C⁺是N3-质子化胞嘧啶)提供了对齐位点,而GpA步中不寻常的链间G-A碱基堆积提供了额外的稳定力。二维核Overhauser效应光谱的可交换质子数据与精炼结构完全一致。我们得出结论,5'-CGA或其他相关序列(如5'-CCGA)是促进II-DNA或II-RNA构象的强大基序,这些构象可能发挥某些生物学功能。