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• Review •

The Role of Aliphatic Chains in Pyrrole-Imidazole Polyamides and Their Conjugates Binding to DNA

Jiang Shikun1, Wang Pu1, Wu Yanling2, Zhang Wen1   

  1. 1. Department of Biopharmaceutical Sciences, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China;
    2. Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
  • Received: Revised: Online: Published:
  • Contact: Wang Pu, Zhang Wen E-mail:wzhang63@zjut.edu.cn; wangpu@zjut.edu.cn
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The pyrrole-imidazole (Py-Im) polyamides represent the only available class of synthetic small molecules which can be designed to recognize virtually any predetermined B-DNA sequence in minor groove and permeate into nucleus to regulate gene expression in vitro & in vivo due to affinities and specificities, and equal or exceed natural eukaryotic transcriptional regulatory proteins. They are mainly composed of N-methylpyrrole (Py), N-methylimidazole (Im), N-methyl-3-hydroxypyrrole (Hp) amino acids and aliphatic chain compounds including aliphatic amino acids. In these moieties, an aliphatic chain as a part of constructing polyamides and their conjugates plays a very important role in extending and specifically recognizing predetermined DNA sequences, linking functioned bioactive molecules to polyamides, and gene regulation. Understanding the role of aliphatic chains in polyamides and their conjugates may help us to better design suitable polyamides to be applied in DNA recognition,which can speed up research of polyamides as a gene-targeted clinical drug. In this paper, we review the application of aliphatic chains of polyamides and their conjugates in polyamides binding to B-DNA minor groove and analyze existing problems.

Contents
1 Introduction
2 The effect of γ-aminobutyric acid and its structural variants on interaction of polyamides with DNA
2.1 Role of γ-aminobutyric acid in DNA recognition by polyamides
2.2 The effect of structural modification with γ-aminobutyric acid on DNA recognition affinity and specificity by polyamides
2.3 The effect of cyclic polyamides linked by γ-aminobutyric acid on DNA recognition
3 The effect of β-alanine and its structural variants on interaction of polyamides with DNA
3.1 Role of β-alanine in DNA recognition by polyamides
3.2 The influence of β-alanine structural modification on DNA recognition by polyamides
4 Role of aliphatic chains in unusual structural polyamides
5 Role of the linkers of polyamides in biological application
5.1 Role of the linkers in polyamide-fluorophore conjugates
5.2 Role of the linkers in polyamide-alkylating agent conjugates
5.3 Role of the linkers of polyamides in gene regulation
6 Conclusion and outlook

 

Key words: aliphatic chains, Py-Im polyamides, conjugates, B-DNA

CLC Number: 

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