1l3m: Difference between revisions

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[[Image:1l3m.gif|left|200px]]<br /><applet load="1l3m" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[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.

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://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1L3M OCA].

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==

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: Cheng, J W.]]

[[Category: Chou, S.H.]]

[[Category: Chou, S H.]]

[[Category: Hsu, S.T.]]

[[Category: Hsu, S T.]]

[[Category: Huang, W.C.]]

[[Category: Huang, W C.]]

[[Category: Jain, M.L.]]

[[Category: Jain, M L.]]

[[Category: Tsao, Y.P.]]

[[Category: Tsao, Y P.]]

[[Category: Wang, L.Y.]]

[[Category: Wang, L Y.]]

[[Category: 2'o-methyl]]

[[Category: chimeric duplex]]

[[Category: dna/rna hybrid]]

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@@ Line 1: / Line 1: @@
-[[Image:1l3m.gif|left|200px]]<br /><applet load="1l3m" size="450" color="white" frame="true" align="right" spinBox="true"
+[[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.
+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==
-L3M 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1L3M OCA].
+L3M 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==
 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: Cheng, J W.]]
-[[Category: Chou, S.H.]]
+[[Category: Chou, S H.]]
-[[Category: Hsu, S.T.]]
+[[Category: Hsu, S T.]]
-[[Category: Huang, W.C.]]
+[[Category: Huang, W C.]]
-[[Category: Jain, M.L.]]
+[[Category: Jain, M L.]]
-[[Category: Tsao, Y.P.]]
+[[Category: Tsao, Y P.]]
-[[Category: Wang, L.Y.]]
+[[Category: Wang, L Y.]]
 [[Category: 2'o-methyl]]
 [[Category: chimeric duplex]]
 [[Category: dna/rna hybrid]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:26:44 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:40:55 2008''