1L3M

The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2

Summary for 1L3M

• Entry DOI: 10.2210/pdb1l3m/pdb
• Descriptor: 5'-D(*CP*GP*C)-R(P*(A39)P*(A39)P*(A39))-D(P*TP*TP*TP*GP*CP*G)-3' (1 entity in total)
• Functional Keywords: dna/rna hybrid, chimeric duplex, 2'o-methyl, dna-rna complex, dna/rna
• Total number of polymer chains: 2
• Total formula weight: 7504.96

Authors

Tsao, Y.P.,Wang, L.Y.,Hsu, S.T.,Jain, M.L.,Chou, S.H.,Huang, W.C.,Cheng, J.W. (deposition date: 2002-02-28, release date: 2002-04-03, Last modification date: 2024-05-01)

Primary citation

Tsao, Y.P.,Wang, L.Y.,Hsu, S.T.,Jain, M.L.,Chou, S.H.,Huang, C.,Cheng, J.W.
The solution structure of [d(CGC)r(amamam)d(TTTGCG)]2.
J.Biomol.NMR, 21:209-220, 2001

PubMed Abstract: 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.

PubMed: 11775738
DOI: 10.1023/A:1012924932513

Experimental method

SOLUTION NMR