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三核苷酸重复序列d(GTC)15呈发夹构象。

The trinucleotide repeat sequence d(GTC)15 adopts a hairpin conformation.

作者信息

Yu A, Dill J, Wirth S S, Huang G, Lee V H, Haworth I S, Mitas M

机构信息

Department of Biochemistry and Molecular Biology, Oklahoma State University, Noble Research Center Stillwater 74078, USA.

出版信息

Nucleic Acids Res. 1995 Jul 25;23(14):2706-14. doi: 10.1093/nar/23.14.2706.

DOI:10.1093/nar/23.14.2706
PMID:7651831
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC307095/
Abstract

The structure of a single-stranded (ss) oligonucleotide containing (GTC)15 [ss(GTC)15] was examined. As a control, parallel studies were performed with ss(CTG)15, an oligonucleotide that forms a hairpin. Electrophoretic mobility, KMnO4 oxidation and P1 nuclease studies demonstrate that, similar to ss(CTG)15, ss(GTC)15 forms a hairpin containing base paired and/or stacked thymines in the stem. Electrophoretic mobility melting profiles performed in approximately 1 mM Na+ revealed that the melting temperature of ss(GTC)15 and ss(CTG)15 were 38 and 48 degrees C respectively. The loop regions of ss(GTC)15 and ss(CTG)15 were cleaved by single-strand-specific P1 nuclease at the T25-C29 and G26-C27 phosphodiester bonds respectively (where the loop apex of the DNAs is T28). Molecular dynamics simulations suggested that in ss(GTC)15 the loop was bent towards the major groove of the stem, apparently causing an increased exposure of the T25-C29 region to solvent. In ss(CTG)15 guanine--guanine stacking caused a separation of the G26 and C27 bases, resulting in exposure of the intervening phosphodiester to solvent. The results suggest that ss(GTC)15 and ss(CTG)15 form similar, but distinguishable, hairpin structures.

摘要

对含有(GTC)15的单链(ss)寡核苷酸[ss(GTC)15]的结构进行了研究。作为对照，对ss(CTG)15进行了平行研究，ss(CTG)15是一种形成发夹结构的寡核苷酸。电泳迁移率、高锰酸钾氧化和P1核酸酶研究表明，与ss(CTG)15类似，ss(GTC)15形成了一个在茎中含有碱基配对和/或堆积胸腺嘧啶的发夹结构。在约1 mM Na+条件下进行的电泳迁移率熔解曲线表明，ss(GTC)15和ss(CTG)15的熔解温度分别为38和48摄氏度。ss(GTC)15和ss(CTG)15的环区分别被单链特异性P1核酸酶在T25 - C29和G26 - C27磷酸二酯键处切割(其中DNA的环顶点为T28)。分子动力学模拟表明，在ss(GTC)15中，环向茎的大沟弯曲，显然导致T25 - C29区域对溶剂的暴露增加。在ss(CTG)15中，鸟嘌呤 - 鸟嘌呤堆积导致G26和C27碱基分离，导致中间的磷酸二酯暴露于溶剂中。结果表明，ss(GTC)15和ss(CTG)15形成了相似但可区分的发夹结构。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/4563155a46fc/nar00014-0151-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/332d5ce377f6/nar00014-0146-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/f6ad6450765f/nar00014-0147-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/df059fabe94b/nar00014-0148-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/a5d6b8e16efe/nar00014-0148-b.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/818918c516e8/nar00014-0149-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/b320e6bccc99/nar00014-0149-b.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/2b4f764f8313/nar00014-0150-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/b4b16427db12/nar00014-0150-b.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/4563155a46fc/nar00014-0151-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/332d5ce377f6/nar00014-0146-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/f6ad6450765f/nar00014-0147-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/df059fabe94b/nar00014-0148-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/a5d6b8e16efe/nar00014-0148-b.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/818918c516e8/nar00014-0149-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/b320e6bccc99/nar00014-0149-b.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/2b4f764f8313/nar00014-0150-a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/b4b16427db12/nar00014-0150-b.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b889/307095/4563155a46fc/nar00014-0151-a.jpg

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