体内的双碱基DNA发夹环结构
Two-base DNA hairpin-loop structures in vivo.
作者信息
Davison A, Leach D R
机构信息
Institute of Cell and Molecular Biology, University of Edinburgh, UK.
出版信息
Nucleic Acids Res. 1994 Oct 25;22(21):4361-3. doi: 10.1093/nar/22.21.4361.
Abstract
In vitro studies have revealed that DNA hairpin-loops usually contain four unpaired bases. However, a small subset of sequences can form two-base loops. We have previously described an in vivo assay that is sensitive to tight loop formation and have set out to test whether DNA sequences known to form two-base loops in vitro also form tight loops in vivo. It is shown that the sequences 5'dCNNG and 5'dTNNA behave as predicted if they favour two-base loop formation in vivo, a result that is consistent with previously described in vitro studies. The ability of specific DNA sequences to form tight loops in vivo has implications for their potential to form transient structures involved in gene regulation, recombination and mutagenesis.
摘要
体外研究表明，DNA发夹环通常包含四个未配对碱基。然而，一小部分序列可形成双碱基环。我们之前描述了一种对紧密环形成敏感的体内检测方法，并着手测试已知在体外形成双碱基环的DNA序列在体内是否也形成紧密环。结果表明，如果5'dCNNG和5'dTNNA序列在体内倾向于形成双碱基环，那么它们的表现符合预期，这一结果与之前描述的体外研究一致。特定DNA序列在体内形成紧密环的能力对其形成参与基因调控、重组和诱变的瞬时结构的潜力具有重要意义。
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本文引用的文献
1
Unusual DNA structures, chromatin and transcription.
Bioessays. 1994 Jan;16(1):59-68. doi: 10.1002/bies.950160110.
2
The effects of nucleotide sequence changes on DNA secondary structure formation in Escherichia coli are consistent with cruciform extrusion in vivo.
Genetics. 1994 Jun;137(2):361-8. doi: 10.1093/genetics/137.2.361.
3
Evolutionary selection for perfect hairpin structures in viral DNAs.
Nature. 1982 Aug 5;298(5874):582-5. doi: 10.1038/298582a0.
4
Influence of loop residues on the relative stabilities of DNA hairpin structures.
Proc Natl Acad Sci U S A. 1988 Sep;85(17):6242-6. doi: 10.1073/pnas.85.17.6242.
5
Nucleic acids and nuclear magnetic resonance.
Eur J Biochem. 1988 Dec 1;178(1):1-38. doi: 10.1111/j.1432-1033.1988.tb14425.x.
6
Effects of base sequence on the loop folding in DNA hairpins.
Biochemistry. 1989 Sep 5;28(18):7491-8. doi: 10.1021/bi00444a049.
7
Hairpin structures in DNA containing arabinofuranosylcytosine. A combination of nuclear magnetic resonance and molecular dynamics.
Biochemistry. 1990 Jan 23;29(3):788-99. doi: 10.1021/bi00455a029.
8
Cloning and sequence analysis of gyrA gene of Klebsiella pneumoniae.
Nucleic Acids Res. 1990 Jan 11;18(1):151-6. doi: 10.1093/nar/18.1.151.
9
Conformational feasibility of a hairpin with two purines in the loop. 5'-d-GGTACIAGTACC-3'.
Biochemistry. 1991 Jan 22;30(3):782-8. doi: 10.1021/bi00217a031.
10
The three-dimensional structure of a DNA hairpin in solution two-dimensional NMR studies and structural analysis of d(ATCCTATTTATAGGAT).
Eur J Biochem. 1991 Oct 1;201(1):33-51. doi: 10.1111/j.1432-1033.1991.tb16253.x.
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