具有Hoogsteen碱基配对的反平行DNA片段的晶体结构。
Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing.
作者信息
Abrescia Nicola G A, Thompson Andrew, Huynh-Dinh Tam, Subirana Juan A
机构信息
Departament d'Enginyeria Quimica, Universitat Politècnica de Catalunya, Avga Diagonal 647, E-08028 Barcelona, Spain.
出版信息
Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2806-11. doi: 10.1073/pnas.052675499.
Abstract
We report here an alternative double-helical structure of the DNA molecule. It has been found in the d(ATA(Br)UAT) and d(ATATAT) sequences by single-crystal x-ray crystallography. This sequence is found not only in TATA boxes, but also in other regulatory regions of DNA. Bases of the two antiparallel strands form Hoogsteen pairs, with adenines in the syn conformation. The structure is related neither to those found in triple helices nor to parallel DNA duplexes. Its conformational parameters are very similar to those of duplex DNA in the B form. Both forms may coexist under physiological conditions, although the Hoogsteen pairing greatly influences the recognition sites on DNA. Our results demonstrate that an alternative to the classical B-DNA double helix is possible.
摘要
我们在此报告DNA分子的一种替代双螺旋结构。它通过单晶X射线晶体学在d(ATA(Br)UAT)和d(ATATAT)序列中被发现。该序列不仅存在于TATA框中，也存在于DNA的其他调控区域。两条反平行链的碱基形成Hoogsteen配对，腺嘌呤处于顺式构象。该结构既与三螺旋中发现的结构无关，也与平行DNA双链体无关。其构象参数与B型双链DNA的构象参数非常相似。尽管Hoogsteen配对极大地影响了DNA上的识别位点，但两种形式在生理条件下可能共存。我们的结果表明经典B-DNA双螺旋存在替代结构是可能的。
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本文引用的文献
1
Processing of X-ray diffraction data collected in oscillation mode.
Methods Enzymol. 1997;276:307-26. doi: 10.1016/S0076-6879(97)76066-X.
2
X-ray studies on two synthetic DNA copolymers.
J Mol Biol. 1963 Apr;6:251-5. doi: 10.1016/s0022-2836(63)80086-8.
3
Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.
Nature. 1953 Apr 25;171(4356):737-8. doi: 10.1038/171737a0.
4
The first example of a Hoogsteen base-paired DNA duplex in dynamic equilibrium with a Watson-Crick base-paired duplex--a structural (NMR), kinetic and thermodynamic study.
J Biomol Struct Dyn. 2001 Jun;18(6):783-806. doi: 10.1080/07391102.2001.10506707.
5
Conserved geometrical base-pairing patterns in RNA.
Q Rev Biophys. 1998 Nov;31(4):399-455. doi: 10.1017/s0033583599003479.
6
TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.
Genes Dev. 1999 Dec 15;13(24):3217-30. doi: 10.1101/gad.13.24.3217.
7
Structure of the oligonucleotide d(CGTATATACG) as a site-specific complex with nickel ions.
Nucleic Acids Res. 1999 Apr 1;27(7):1593-9. doi: 10.1093/nar/27.7.1593.
8
Crystallography & NMR system: A new software suite for macromolecular structure determination.
Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21. doi: 10.1107/s0907444998003254.
9
Homopurine and homopyrimidine strands complementary in parallel orientation form an antiparallel duplex at neutral pH with A-C, G-T, and T-C mismatched base pairs.
Biopolymers. 1997 Jun;41(7):773-84. doi: 10.1002/(SICI)1097-0282(199706)41:7<773::AID-BIP6>3.0.CO;2-M.
10
How proteins recognize the TATA box.
J Mol Biol. 1996 Aug 16;261(2):239-54. doi: 10.1006/jmbi.1996.0456.
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