François J C, Hélène C
Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM Unité 201- CNRS UA 481, 43 rue Cuvier, 75231 Paris Cedex 05, France.
Bioconjug Chem. 1999 May-Jun;10(3):439-46. doi: 10.1021/bc9801225.
Oligodeoxynucleotides with an internal intercalating agent have been targeted to single-stranded sequences containing hairpin structures. The oligonucleotide binds to nonadjacent single-stranded sequences on both sides of the hairpin structure in such a way as to form a three-way junction. The acridine derivative is inserted at a position that allows it to interact with the three-way junction. The melting temperature (Tm) of complexes formed between the hairpin-containing target and oligonucleotides containing one internal acridine derivative was higher than that obtained with the same target and an unmodified oligonucleotide (DeltaTm = +13 degrees C). The internal acridine provided the oligonucleotide with a higher affinity than covalent attachment to the 5' end. Oligonucleotides could also be designed to recognize a hairpin-containing single-stranded nucleic acid by formation of Watson-Crick hydrogen bonds with a single-stranded part and Hoogsteen hydrogen bonds with the stem of the hairpin. An internal acridine derivative was introduced at the junction between the two domains, the double helix domain with Watson-Crick base pairs and the triple helix domain involving Hoogsteen base triplets in the major groove of the hairpin stem. Oligonucleotides with an internal acridine or an acridine at their 5' end have similar binding affinities for the stem-loop-containing target. The bis-modified oligonucleotide containing two acridines, one at the 5' end and one at an internal site, did not exhibit a higher affinity than the oligonucleotides with only one intercalating agent. The design of oligonucleotides with an internal intercalating agent might be of interest to control gene expression through recognition of secondary structures in single-stranded targets.
带有内部嵌入剂的寡脱氧核苷酸已被靶向含有发夹结构的单链序列。寡核苷酸以形成三链连接的方式与发夹结构两侧不相邻的单链序列结合。吖啶衍生物插入到一个使其能够与三链连接相互作用的位置。含有一个内部吖啶衍生物的寡核苷酸与含发夹结构的靶标形成的复合物的解链温度（Tm）高于相同靶标与未修饰寡核苷酸形成的复合物的解链温度（ΔTm = +13℃）。内部吖啶赋予寡核苷酸的亲和力高于其与5'端的共价连接。寡核苷酸也可设计成通过与单链部分形成沃森-克里克氢键以及与发夹茎形成 hoogsteen 氢键来识别含发夹结构的单链核酸。在两个结构域之间的连接处引入内部吖啶衍生物，这两个结构域分别是具有沃森-克里克碱基对的双螺旋结构域和涉及发夹茎大沟中 hoogsteen 碱基三联体的三螺旋结构域。在5'端带有内部吖啶或吖啶的寡核苷酸对含茎环结构的靶标具有相似的结合亲和力。含有两个吖啶（一个在5'端，一个在内部位点）的双修饰寡核苷酸并未表现出比仅含有一个嵌入剂的寡核苷酸更高的亲和力。设计带有内部嵌入剂的寡核苷酸可能对于通过识别单链靶标中的二级结构来控制基因表达具有重要意义。
