1l3m
From Proteopedia
(New page: 200px<br /><applet load="1l3m" size="450" color="white" frame="true" align="right" spinBox="true" caption="1l3m" /> '''The Solution Structure of [d(CGC)r(amamam)d(...) |
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'''The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2'''<br /> | '''The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The solution structure and hydration of a DNA.RNA hybrid chimeric duplex | + | 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== | ==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:// | + | 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]. |
==Reference== | ==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11775738 11775738] | 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: Protein complex]] | ||
| - | [[Category: Cheng, J | + | [[Category: Cheng, J W.]] |
| - | [[Category: Chou, S | + | [[Category: Chou, S H.]] |
| - | [[Category: Hsu, S | + | [[Category: Hsu, S T.]] |
| - | [[Category: Huang, W | + | [[Category: Huang, W C.]] |
| - | [[Category: Jain, M | + | [[Category: Jain, M L.]] |
| - | [[Category: Tsao, Y | + | [[Category: Tsao, Y P.]] |
| - | [[Category: Wang, L | + | [[Category: Wang, L Y.]] |
[[Category: 2'o-methyl]] | [[Category: 2'o-methyl]] | ||
[[Category: chimeric duplex]] | [[Category: chimeric duplex]] | ||
[[Category: dna/rna hybrid]] | [[Category: dna/rna hybrid]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:40:55 2008'' |
Revision as of 11:40, 21 February 2008
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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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