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杂交肽核酸-脱氧核糖核酸（PNA-DNA）四链体连接体的结构及蛋白质识别特性表征

Characterization of the structural and protein recognition properties of hybrid PNA-DNA four-way junctions.

作者信息

Iverson Douglas, Serrano Crystal, Brahan Ann Marie, Shams Arik, Totsingan Filbert, Bell Anthony J

机构信息

Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS, USA.

Department of Chemistry, New York University, New York, NY, USA.

出版信息

Arch Biochem Biophys. 2015 Dec 1;587:1-11. doi: 10.1016/j.abb.2015.08.017. Epub 2015 Sep 5.

DOI:10.1016/j.abb.2015.08.017
PMID:26348651
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4852880/
Abstract

The objective of this study is to evaluate the structure and protein recognition properties of hybrid four-way junctions (4WJs) composed of DNA and peptide nucleic acid (PNA) strands. We compare a classic immobile DNA junction, J1, vs. six PNA-DNA junctions, including a number with blunt DNA ends and multiple PNA strands. Circular dichroism (CD) analysis reveals that hybrid 4WJs are composed of helices that possess structures intermediate between A- and B-form DNA, the apparent level of A-form structure correlates with the PNA content. The structure of hybrids that contain one PNA strand is sensitive to Mg(+2). For these constructs, the apparent B-form structure and conformational stability (Tm) increase in high Mg(+2). The blunt-ended junction, b4WJ-PNA3, possesses the highest B-form CD signals and Tm (40.1 °C) values vs. all hybrids and J1. Protein recognition studies are carried out using the recombinant DNA-binding protein, HMGB1b. HMGB1b binds the blunt ended single-PNA hybrids, b4WJ-PNA1 and b4WJ-PNA3, with high affinity. HMGB1b binds the multi-PNA hybrids, 4WJ-PNA1,3 and b4WJ-PNA1,3, but does not form stable protein-nucleic acid complexes. Protein interactions with hybrid 4WJs are influenced by the ratio of A- to B-form helices: hybrids with helices composed of higher levels of B-form structure preferentially associate with HMGB1b.

摘要

本研究的目的是评估由DNA和肽核酸（PNA）链组成的杂合四链体连接点（4WJ）的结构和蛋白质识别特性。我们比较了经典的固定DNA连接点J1与六个PNA-DNA连接点，包括一些具有平端DNA末端和多条PNA链的连接点。圆二色性（CD）分析表明，杂合4WJ由具有介于A-型和B-型DNA之间结构的螺旋组成，A-型结构的表观水平与PNA含量相关。含有一条PNA链的杂合体结构对Mg(+2)敏感。对于这些构建体，在高Mg(+2)条件下，表观B-型结构和构象稳定性（Tm）增加。平端连接点b4WJ-PNA3与所有杂合体和J1相比，具有最高的B-型CD信号和Tm（40.1°C）值。使用重组DNA结合蛋白HMGB1b进行蛋白质识别研究。HMGB1b以高亲和力结合平端单PNA杂合体b4WJ-PNA1和b4WJ-PNA3。HMGB1b结合多PNA杂合体4WJ-PNA1,3和b4WJ-PNA1,3，但不形成稳定的蛋白质-核酸复合物。蛋白质与杂合4WJ的相互作用受A-型与B-型螺旋比例的影响：具有由较高水平B-型结构组成的螺旋的杂合体优先与HMGB1b结合。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/367cf6ba7880/nihms731227f8.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/fc3341dd1899/nihms731227f4.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/17fa3e77f1b6/nihms731227f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/56082ff3400e/nihms731227f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/367cf6ba7880/nihms731227f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/81bf8b3cfcb3/nihms731227f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/9481fe203224/nihms731227f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/42304ae85835/nihms731227f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/fc3341dd1899/nihms731227f4.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/17fa3e77f1b6/nihms731227f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/56082ff3400e/nihms731227f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e207/4852880/367cf6ba7880/nihms731227f8.jpg

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