1l3m

[[Image:1l3m.gif|left|200px]]<br /><applet load="1l3m" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1l3m" />

'''The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2'''<br />

==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 [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L3M OCA].

 

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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11775738 11775738]

[[Category: Protein complex]]

[[Category: Cheng, J W.]]

[[Category: Chou, S H.]]

[[Category: Hsu, S T.]]

[[Category: Huang, W C.]]

[[Category: Jain, M L.]]

[[Category: Tsao, Y P.]]

[[Category: Wang, L Y.]]