1g2j
From Proteopedia
(New page: 200px<br /><applet load="1g2j" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g2j, resolution 1.97Å" /> '''RNA OCTAMER R(CCCP*G...) |
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| - | [[Image:1g2j.gif|left|200px]]<br /><applet load="1g2j" size=" | + | [[Image:1g2j.gif|left|200px]]<br /><applet load="1g2j" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1g2j, resolution 1.97Å" /> | caption="1g2j, resolution 1.97Å" /> | ||
'''RNA OCTAMER R(CCCP*GGGG) CONTAINING PHENYL RIBONUCLEOTIDE'''<br /> | '''RNA OCTAMER R(CCCP*GGGG) CONTAINING PHENYL RIBONUCLEOTIDE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Chemically modified nucleotide analogs have gained widespread popularity | + | Chemically modified nucleotide analogs have gained widespread popularity for probing structure-function relationships. Among the modifications that were incorporated into RNAs for assessing the role of individual functional groups, the phenyl nucleotide has displayed surprising effects both in the contexts of the hammerhead ribozyme and pre-mRNA splicing. To examine the conformational properties of this hydrophobic base analog, we determined the crystal structure of an RNA double helix with incorporated phenyl ribonucleotides at 1.97 A resolution. In the structure, phenyl residues are engaged in self-pairing and their arrangements suggest energetically favorable stacking interactions with 3'-adjacent guanines. The presence of the phenyl rings in the center of the duplex results in only moderate changes of the helical geometry. This finding is in line with those of earlier experiments that showed the phenyl analog to be a remarkably good mimetic of natural base function. Because the stacking interactions displayed by phenyl residues appear to be similar to those for natural bases, reduced conformational restriction due to the lack of hydrogen bonds with phenyl as well as alterations in its solvent structure may be the main causes of the activity changes with phenyl-modified RNAs. |
==About this Structure== | ==About this Structure== | ||
| - | 1G2J is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1G2J is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G2J OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Minasov, G.]] | [[Category: Minasov, G.]] | ||
[[Category: Usman, N.]] | [[Category: Usman, N.]] | ||
| - | [[Category: Wilds, C | + | [[Category: Wilds, C J.]] |
[[Category: CA]] | [[Category: CA]] | ||
[[Category: phenyl-ribonucleotide]] | [[Category: phenyl-ribonucleotide]] | ||
[[Category: rna duplex]] | [[Category: rna duplex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:45:20 2008'' |
Revision as of 10:45, 21 February 2008
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RNA OCTAMER R(CCCP*GGGG) CONTAINING PHENYL RIBONUCLEOTIDE
Overview
Chemically modified nucleotide analogs have gained widespread popularity for probing structure-function relationships. Among the modifications that were incorporated into RNAs for assessing the role of individual functional groups, the phenyl nucleotide has displayed surprising effects both in the contexts of the hammerhead ribozyme and pre-mRNA splicing. To examine the conformational properties of this hydrophobic base analog, we determined the crystal structure of an RNA double helix with incorporated phenyl ribonucleotides at 1.97 A resolution. In the structure, phenyl residues are engaged in self-pairing and their arrangements suggest energetically favorable stacking interactions with 3'-adjacent guanines. The presence of the phenyl rings in the center of the duplex results in only moderate changes of the helical geometry. This finding is in line with those of earlier experiments that showed the phenyl analog to be a remarkably good mimetic of natural base function. Because the stacking interactions displayed by phenyl residues appear to be similar to those for natural bases, reduced conformational restriction due to the lack of hydrogen bonds with phenyl as well as alterations in its solvent structure may be the main causes of the activity changes with phenyl-modified RNAs.
About this Structure
1G2J is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Crystal structure of an RNA duplex containing phenyl-ribonucleotides, hydrophobic isosteres of the natural pyrimidines., Minasov G, Matulic-Adamic J, Wilds CJ, Haeberli P, Usman N, Beigelman L, Egli M, RNA. 2000 Nov;6(11):1516-28. PMID:11105752
Page seeded by OCA on Thu Feb 21 12:45:20 2008
