Ulyanov N B, Ivanov V I, Minyat E E, Khomyakova E B, Petrova M V, Lesiak K, James T L
Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA.
Biochemistry. 1998 Sep 15;37(37):12715-26. doi: 10.1021/bi981018d.
We report a high-resolution NMR structure of a homodimer formed by a synthetic 25 residue DNA oligonucleotide GCTCCCATGGTTTTTGTGCACGAGC. This structure presents a novel structural motif for single-stranded nucleic acids, called a pseudosquare knot (PSQ). The oligonucleotide was originally designed to mimic a slipped-loop structure (SLS), another "unusual" DNA structure postulated as an alternative conformation for short direct repeats in double-stranded DNA. The design of the sequence is compatible with both SLS and PSQ structures, both of which possess identical sets of base-paired and unpaired nucleotides but different tertiary folds. We used deuteration of the H8 positions of purines to ascertain that the PSQ is actually formed under the conditions used. The PSQ structure was solved based on homonuclear proton nuclear Overhauser effect data using complete relaxation matrix methods. The structure essentially consists of two side-by-side helices connected by single-stranded loops. Each of the helices is well-defined; however, the relative orientation of the two remains undetermined by the NMR data. The sequences compatible with the PSQ formation are frequent in single-stranded genomes; this structure may play a role as a dimerization motif.
我们报道了由合成的25个残基的DNA寡核苷酸GCTCCCATGGTTTTTGTGCACGAGC形成的同型二聚体的高分辨率核磁共振结构。该结构呈现出一种单链核酸的新型结构基序，称为假方结（PSQ）。该寡核苷酸最初设计用于模拟滑环结构（SLS），另一种“异常”的DNA结构，被假定为双链DNA中短直接重复序列的替代构象。该序列的设计与SLS和PSQ结构均兼容，这两种结构都具有相同的碱基配对和未配对核苷酸集，但三级折叠不同。我们利用嘌呤H8位置的氘代来确定PSQ实际上是在所使用的条件下形成的。基于同核质子核Overhauser效应数据，采用完全弛豫矩阵方法解析了PSQ结构。该结构主要由通过单链环连接的两个并排螺旋组成。每个螺旋都定义明确；然而，NMR数据尚未确定两者的相对取向。与PSQ形成兼容的序列在单链基因组中很常见；这种结构可能作为二聚化基序发挥作用。
