1G2J

RNA OCTAMER R(CCCP*GGGG) CONTAINING PHENYL RIBONUCLEOTIDE

Summary for 1G2J

• Entry DOI: 10.2210/pdb1g2j/pdb
• Descriptor: 5'-R(*CP*CP*CP*(PYY)P*GP*GP*GP*G)-3', CALCIUM ION (3 entities in total)
• Functional Keywords: rna duplex, phenyl-ribonucleotide, rna
• Total number of polymer chains: 1
• Total formula weight: 2603.76

Authors

Minasov, G.,Matulic-Adamic, J.,Wilds, C.J.,Haeberli, P.,Usman, N.,Beigelman, L.,Egli, M. (deposition date: 2000-10-20, release date: 2000-12-06, Last modification date: 2024-04-03)

Primary citation

Minasov, G.,Matulic-Adamic, J.,Wilds, C.J.,Haeberli, P.,Usman, N.,Beigelman, L.,Egli, M.
Crystal structure of an RNA duplex containing phenyl-ribonucleotides, hydrophobic isosteres of the natural pyrimidines.
RNA, 6:1516-1528, 2000

PubMed Abstract: 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.

PubMed: 11105752
DOI: 10.1017/S1355838200001114

Experimental method

X-RAY DIFFRACTION (1.97 Å)