1w86
From Proteopedia
(New page: 200px<br /><applet load="1w86" size="450" color="white" frame="true" align="right" spinBox="true" caption="1w86" /> '''SOLUTION STRUCTURE OF AN DSDNA:LNA TRIPLEX''...) |
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| - | [[Image:1w86.gif|left|200px]]<br /><applet load="1w86" size=" | + | [[Image:1w86.gif|left|200px]]<br /><applet load="1w86" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1w86" /> | caption="1w86" /> | ||
'''SOLUTION STRUCTURE OF AN DSDNA:LNA TRIPLEX'''<br /> | '''SOLUTION STRUCTURE OF AN DSDNA:LNA TRIPLEX'''<br /> | ||
==Overview== | ==Overview== | ||
| - | We have determined the NMR structure of an intramolecular dsDNA:LNA | + | We have determined the NMR structure of an intramolecular dsDNA:LNA triplex, where the LNA strand is composed of alternating LNA and DNA nucleotides. The LNA oligonucleotide binds to the dsDNA duplex in the major groove by formation of Hoogsteen hydrogen bonds to the purine strand of the duplex. The structure of the dsDNA duplex is changed to accommodate the LNA strand, and it adopts a geometry intermediate between A- and B-type. There is a substantial propeller twist between base-paired nucleobases. This propeller twist and a concomitant large propeller twist between the purine and LNA strands allows the pyrimidines of the LNA strand to interact with the 5'-flanking duplex pyrimidines. Altogether, the triplex has a regular global geometry as shown by a straight helix axis. This shows that even though the third strand is composed of alternating DNA and LNA monomers with different sugar puckers, it forms a seamless triplex. The thermostability of the triplex is increased by 19 degrees C relative to the unmodified DNA triplex at acidic pH. Using NMR spectroscopy, we show that the dsDNA:LNA triplex is stable at pH 8, and that the triplex structure is identical to the structure determined at pH 5.1. |
==About this Structure== | ==About this Structure== | ||
| - | 1W86 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1W86 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W86 OCA]. |
==Reference== | ==Reference== | ||
Solution structure of a dsDNA:LNA triplex., Sorensen JJ, Nielsen JT, Petersen M, Nucleic Acids Res. 2004 Nov 18;32(20):6078-85. Print 2004. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15550567 15550567] | Solution structure of a dsDNA:LNA triplex., Sorensen JJ, Nielsen JT, Petersen M, Nucleic Acids Res. 2004 Nov 18;32(20):6078-85. Print 2004. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15550567 15550567] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Nielsen, J | + | [[Category: Nielsen, J T.]] |
[[Category: Petersen, M.]] | [[Category: Petersen, M.]] | ||
| - | [[Category: Sorensen, J | + | [[Category: Sorensen, J J.]] |
[[Category: dna]] | [[Category: dna]] | ||
[[Category: lna]] | [[Category: lna]] | ||
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[[Category: triplex]] | [[Category: triplex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:41:32 2008'' |
Revision as of 13:41, 21 February 2008
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SOLUTION STRUCTURE OF AN DSDNA:LNA TRIPLEX
Overview
We have determined the NMR structure of an intramolecular dsDNA:LNA triplex, where the LNA strand is composed of alternating LNA and DNA nucleotides. The LNA oligonucleotide binds to the dsDNA duplex in the major groove by formation of Hoogsteen hydrogen bonds to the purine strand of the duplex. The structure of the dsDNA duplex is changed to accommodate the LNA strand, and it adopts a geometry intermediate between A- and B-type. There is a substantial propeller twist between base-paired nucleobases. This propeller twist and a concomitant large propeller twist between the purine and LNA strands allows the pyrimidines of the LNA strand to interact with the 5'-flanking duplex pyrimidines. Altogether, the triplex has a regular global geometry as shown by a straight helix axis. This shows that even though the third strand is composed of alternating DNA and LNA monomers with different sugar puckers, it forms a seamless triplex. The thermostability of the triplex is increased by 19 degrees C relative to the unmodified DNA triplex at acidic pH. Using NMR spectroscopy, we show that the dsDNA:LNA triplex is stable at pH 8, and that the triplex structure is identical to the structure determined at pH 5.1.
About this Structure
1W86 is a Single protein structure of sequence from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of a dsDNA:LNA triplex., Sorensen JJ, Nielsen JT, Petersen M, Nucleic Acids Res. 2004 Nov 18;32(20):6078-85. Print 2004. PMID:15550567
Page seeded by OCA on Thu Feb 21 15:41:32 2008
Categories: Single protein | Nielsen, J T. | Petersen, M. | Sorensen, J J. | Dna | Lna | Nmr spectroscopy | Structure | Triplex
