1l3m
From Proteopedia
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The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2
Overview
The solution structure and hydration of a DNA.RNA hybrid chimeric duplex, [d(CGC)r(amamam)d(TTTGCG)]2 in which the RNA adenines were substituted by, 2'-O-methylated riboadenines was determined using two-dimensional NMR, simulated annealing, and restrained molecular dynamics. Only DNA residue, 7T in the 2'-OMe-RNA.DNA junction adopted an O4'-endo sugar conformation, while the other DNA residues including 3C in the DNA.2'-OMe-RNA junction, adopted C1'-exo or C2'-endo conformations. The observed NOE intensity of, 2'-O-methyl group to H1' proton of 4am at the DNA.2'-OMe-RNA junction is, much weaker than those of 5am and 6am. The 2'-O-methyl group of 4am was, found to orient towards the minor groove in the trans domain while the, 2'-O-methyl groups of 5am and 6am were found to be in the gauche (+), domain. In contrast to the long-lived water molecules found close to the, RNA adenine H2 and H1' protons and the methyl group of 7T in the RNA-DNA, junction of [d(CGC)r(aaa)d(TTTGCG)]2, there were no long-lived water, molecules found in [d(CGC)r(amamam)d(TTTGCG)]2. This is probably due to, the hydrophobic enviroment created by the 2'-O-methylated riboadenines in, the minor groove or due to the wider minor groove width in the middle of, the structure. In addition, the 2'-O-methylation of riboadenines in pure, chimeric duplex increses its melting temperature from 48.5 degrees C to, 51.9 degrees C. The characteristic structural features and hydration, patterns of this chimeric duplex provide a molecular basis for further, therapeutic applications of DNA.RNA hybrid and chimeric duplexes with, 2'-modified RNA residues.
About this Structure
1L3M is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
The solution structure of [d(CGC)r(amamam)d(TTTGCG)]2., Tsao YP, Wang LY, Hsu ST, Jain ML, Chou SH, Huang C, Cheng JW, J Biomol NMR. 2001 Nov;21(3):209-20. PMID:11775738
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