124d
From Proteopedia
(New page: 200px<br /><applet load="124d" size="450" color="white" frame="true" align="right" spinBox="true" caption="124d" /> '''STRUCTURE OF A DNA:RNA HYBRID DUPLEX: WHY RN...) |
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| - | [[Image:124d.jpg|left|200px]]<br /><applet load="124d" size=" | + | [[Image:124d.jpg|left|200px]]<br /><applet load="124d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="124d" /> | caption="124d" /> | ||
'''STRUCTURE OF A DNA:RNA HYBRID DUPLEX: WHY RNASE H DOES NOT CLEAVE PURE RNA'''<br /> | '''STRUCTURE OF A DNA:RNA HYBRID DUPLEX: WHY RNASE H DOES NOT CLEAVE PURE RNA'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The solution structure of the DNA:RNA hybrid duplex | + | The solution structure of the DNA:RNA hybrid duplex d(GTCACATG):r(caugugac) has been determined by means of two-dimensional nuclear Overhauser effect (2D-NOE) spectra, restrained molecular dynamics and full-relaxation matrix stimulation of the 2D-NOE spectra. The DNA:RNA hybrid duplex assumes neither an A-form nor a B-form structure in solution, but an intermediate heteromerous duplex structure. The sugars of the RNA strand have a normal N-type C3'-endo conformation, but the DNA strand sugars have neither N-type nor S-type conformations; instead, they have an unexpected intermediate O4'-endo conformation. The negative x-displacement, as well as the small rise and positive inclination of the base-pairs, resembles A-form morphology but the minor groove width is intermediate between that of A-form and B-form duplexes. Both the DNA and RNA strands show prominent sequence-dependent variations in their helical parameters. Combined analysis of NOE and J-coupling data indicates that the DNA sugars are not in a dynamical two-state equilibrium. The detailed three-dimensional structure of this DNA:RNA hybrid molecule leads to a proposed model for its interaction with RNase H. Several specific structural features of the enzyme complexed with the hybrid duplex appear to explain the mechanism whereby RNase H discriminates between DNA:RNA hybrid duplexes and pure RNA:RNA duplexes. |
==About this Structure== | ==About this Structure== | ||
| - | 124D 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:// | + | 124D 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=124D OCA]. |
==Reference== | ==Reference== | ||
Structure of a DNA:RNA hybrid duplex. Why RNase H does not cleave pure RNA., Fedoroff OYu, Salazar M, Reid BR, J Mol Biol. 1993 Oct 5;233(3):509-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8411159 8411159] | Structure of a DNA:RNA hybrid duplex. Why RNase H does not cleave pure RNA., Fedoroff OYu, Salazar M, Reid BR, J Mol Biol. 1993 Oct 5;233(3):509-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8411159 8411159] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Fedoroff, O | + | [[Category: Fedoroff, O Y.]] |
| - | [[Category: Reid, B | + | [[Category: Reid, B R.]] |
[[Category: Salazar, M.]] | [[Category: Salazar, M.]] | ||
[[Category: dna/rna complex]] | [[Category: dna/rna complex]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:37:48 2008'' |
Revision as of 09:37, 21 February 2008
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STRUCTURE OF A DNA:RNA HYBRID DUPLEX: WHY RNASE H DOES NOT CLEAVE PURE RNA
Overview
The solution structure of the DNA:RNA hybrid duplex d(GTCACATG):r(caugugac) has been determined by means of two-dimensional nuclear Overhauser effect (2D-NOE) spectra, restrained molecular dynamics and full-relaxation matrix stimulation of the 2D-NOE spectra. The DNA:RNA hybrid duplex assumes neither an A-form nor a B-form structure in solution, but an intermediate heteromerous duplex structure. The sugars of the RNA strand have a normal N-type C3'-endo conformation, but the DNA strand sugars have neither N-type nor S-type conformations; instead, they have an unexpected intermediate O4'-endo conformation. The negative x-displacement, as well as the small rise and positive inclination of the base-pairs, resembles A-form morphology but the minor groove width is intermediate between that of A-form and B-form duplexes. Both the DNA and RNA strands show prominent sequence-dependent variations in their helical parameters. Combined analysis of NOE and J-coupling data indicates that the DNA sugars are not in a dynamical two-state equilibrium. The detailed three-dimensional structure of this DNA:RNA hybrid molecule leads to a proposed model for its interaction with RNase H. Several specific structural features of the enzyme complexed with the hybrid duplex appear to explain the mechanism whereby RNase H discriminates between DNA:RNA hybrid duplexes and pure RNA:RNA duplexes.
About this Structure
124D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of a DNA:RNA hybrid duplex. Why RNase H does not cleave pure RNA., Fedoroff OYu, Salazar M, Reid BR, J Mol Biol. 1993 Oct 5;233(3):509-23. PMID:8411159
Page seeded by OCA on Thu Feb 21 11:37:48 2008
