327d
From Proteopedia
(New page: 200px<br /><applet load="327d" size="350" color="white" frame="true" align="right" spinBox="true" caption="327d, resolution 1.940Å" /> '''CRYSTAL STRUCTURES ...) |
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==Overview== | ==Overview== | ||
| - | It is well known that methylation of alternating Py x Pu sequences | + | It is well known that methylation of alternating Py x Pu sequences potentiates the formation of Z-DNA. However, we have now observed that methylation of the alternating Z-DNA oligomer d(GCGCGCGCGC), which starts with a 5'-purine, unexpectedly stabilizes the A-DNA conformation. The double methyl derivative d(Gm5CGm5CGCGCGC), which crystallizes as duplex A-DNA in the hexagonal space group P6(1)22, a = b = 39.33 A and c = 77.93 A with one strand per asymmetric unit and six duplexes in the unit cell, refined to an R factor of 19.1 for 204 DNA atoms and 43 solvent molecules. This is the first report of a DNA sequence crystallized in both right and left-handed conformations, allowing structural comparisons not previously possible and, more importantly, this is the first time that methylation has been shown to potentiate the formation of A-DNA from a sequence known to crystallize as Z-DNA. From this study, ten base-pairs appear to be the critical length in determining the handedness of d(GC)n-type sequences in the crystalline state. Because methylation of nuclear DNA is linked to a number of cellular processes, including transcriptional inactivation, this study has important implications for the role of A-DNA in methylated regions of genomic DNA and, thus, in the regulation of gene expression. In this context, the structure of d(Gm5Cm5CGCGCGC) will be compared with that of the alternating A-DNA decamer d(GCACGCGTGC) and the alternating Z-DNA decamer d(GCGCGCGCGC) and discussed in terms of the forces that govern the handedness of duplex DNA oligomers. |
==About this Structure== | ==About this Structure== | ||
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[[Category: Ramakrishnan, B.]] | [[Category: Ramakrishnan, B.]] | ||
[[Category: Sundaralingam, M.]] | [[Category: Sundaralingam, M.]] | ||
| - | [[Category: Tippin, D | + | [[Category: Tippin, D B.]] |
[[Category: a-dna]] | [[Category: a-dna]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: modified]] | [[Category: modified]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:02:02 2008'' |
Revision as of 17:02, 21 February 2008
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CRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC)
Overview
It is well known that methylation of alternating Py x Pu sequences potentiates the formation of Z-DNA. However, we have now observed that methylation of the alternating Z-DNA oligomer d(GCGCGCGCGC), which starts with a 5'-purine, unexpectedly stabilizes the A-DNA conformation. The double methyl derivative d(Gm5CGm5CGCGCGC), which crystallizes as duplex A-DNA in the hexagonal space group P6(1)22, a = b = 39.33 A and c = 77.93 A with one strand per asymmetric unit and six duplexes in the unit cell, refined to an R factor of 19.1 for 204 DNA atoms and 43 solvent molecules. This is the first report of a DNA sequence crystallized in both right and left-handed conformations, allowing structural comparisons not previously possible and, more importantly, this is the first time that methylation has been shown to potentiate the formation of A-DNA from a sequence known to crystallize as Z-DNA. From this study, ten base-pairs appear to be the critical length in determining the handedness of d(GC)n-type sequences in the crystalline state. Because methylation of nuclear DNA is linked to a number of cellular processes, including transcriptional inactivation, this study has important implications for the role of A-DNA in methylated regions of genomic DNA and, thus, in the regulation of gene expression. In this context, the structure of d(Gm5Cm5CGCGCGC) will be compared with that of the alternating A-DNA decamer d(GCACGCGTGC) and the alternating Z-DNA decamer d(GCGCGCGCGC) and discussed in terms of the forces that govern the handedness of duplex DNA oligomers.
About this Structure
327D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Methylation of the Z-DNA decamer d(GC)5 potentiates the formation of A-DNA: crystal structure of d(Gm5CGm5CGCGCGC)., Tippin DB, Ramakrishnan B, Sundaralingam M, J Mol Biol. 1997 Jul 11;270(2):247-58. PMID:9236126
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