1rsb
From Proteopedia
(New page: 200px<br /><applet load="1rsb" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rsb, resolution 2.17Å" /> '''X-ray study of the D...) |
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| - | [[Image:1rsb.gif|left|200px]]<br /><applet load="1rsb" size=" | + | [[Image:1rsb.gif|left|200px]]<br /><applet load="1rsb" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1rsb, resolution 2.17Å" /> | caption="1rsb, resolution 2.17Å" /> | ||
'''X-ray study of the DNA oligomer d(ATATAT) in P65 space group'''<br /> | '''X-ray study of the DNA oligomer d(ATATAT) in P65 space group'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We present and analyze the structure of the oligonucleotide d(ATATAT) | + | We present and analyze the structure of the oligonucleotide d(ATATAT) found in two different forms by X-ray crystallography and in solution by NMR. We find that in both crystal lattices the oligonucleotide forms an antiparallel double helical duplex in which base pairing is of the Hoogsteen type. The double helix is apparently very similar to the standard B-form of DNA, with about 10 base pairs per turn. However, the adenines in the duplex are flipped over; as a result, the physicochemical features of both grooves of the helix are changed. In particular, the minor groove is narrow and hydrophobic. On the other hand, d(ATATAT) displays a propensity to adopt the B conformation in solution. These results confirm the polymorphism of AT-rich sequences in DNA. Furthermore, we show that extrahelical adenines and thymines can be minor groove binders in Hoogsteen DNA. |
==About this Structure== | ==About this Structure== | ||
| - | 1RSB is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1RSB is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RSB OCA]. |
==Reference== | ==Reference== | ||
X-ray and NMR studies of the DNA oligomer d(ATATAT): Hoogsteen base pairing in duplex DNA., Abrescia NG, Gonzalez C, Gouyette C, Subirana JA, Biochemistry. 2004 Apr 13;43(14):4092-100. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15065851 15065851] | X-ray and NMR studies of the DNA oligomer d(ATATAT): Hoogsteen base pairing in duplex DNA., Abrescia NG, Gonzalez C, Gouyette C, Subirana JA, Biochemistry. 2004 Apr 13;43(14):4092-100. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15065851 15065851] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Abrescia, N | + | [[Category: Abrescia, N G.]] |
[[Category: Gonzalez, C.]] | [[Category: Gonzalez, C.]] | ||
[[Category: Gouyette, C.]] | [[Category: Gouyette, C.]] | ||
| - | [[Category: Subirana, J | + | [[Category: Subirana, J A.]] |
[[Category: antiparallel hoogsteen dna]] | [[Category: antiparallel hoogsteen dna]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:54:02 2008'' |
Revision as of 12:54, 21 February 2008
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X-ray study of the DNA oligomer d(ATATAT) in P65 space group
Overview
We present and analyze the structure of the oligonucleotide d(ATATAT) found in two different forms by X-ray crystallography and in solution by NMR. We find that in both crystal lattices the oligonucleotide forms an antiparallel double helical duplex in which base pairing is of the Hoogsteen type. The double helix is apparently very similar to the standard B-form of DNA, with about 10 base pairs per turn. However, the adenines in the duplex are flipped over; as a result, the physicochemical features of both grooves of the helix are changed. In particular, the minor groove is narrow and hydrophobic. On the other hand, d(ATATAT) displays a propensity to adopt the B conformation in solution. These results confirm the polymorphism of AT-rich sequences in DNA. Furthermore, we show that extrahelical adenines and thymines can be minor groove binders in Hoogsteen DNA.
About this Structure
1RSB is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
X-ray and NMR studies of the DNA oligomer d(ATATAT): Hoogsteen base pairing in duplex DNA., Abrescia NG, Gonzalez C, Gouyette C, Subirana JA, Biochemistry. 2004 Apr 13;43(14):4092-100. PMID:15065851
Page seeded by OCA on Thu Feb 21 14:54:02 2008
