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1snj

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{{STRUCTURE_1snj| PDB=1snj | SCENE= }}
{{STRUCTURE_1snj| PDB=1snj | SCENE= }}
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'''Solution structure of the DNA three-way junction with the A/C-stacked conformation'''
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===Solution structure of the DNA three-way junction with the A/C-stacked conformation===
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==Overview==
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Three-way junctions (3H) are the simplest and most commonly occurring branched nucleic acids. They consist of three double helical arms (A to C), connected at the junction point, with or without a number of unpaired bases in one or more of the three different strands. Three-way junctions with two unpaired bases in one strand (3HS2) have a high tendency to adopt either of two alternative stacked conformations in which two of the three arms A, B and C are coaxially stacked, i.e. A/B-stacked or A/C-stacked. Empirical stacking rules, which successfully predict for DNA 3HS2 A/B-stacking preference from sequence, have been extended to A/C-stacked conformations. Three novel DNA 3HS2 sequences were designed to test the validity of these extended stacking rules and their conformational behavior was studied by solution NMR. All three show the predicted A/C-stacking preference even in the absence of multivalent cations. The stacking preference for both classes of DNA 3HS2 can thus be predicted from sequence. The high-resolution NMR solution structure for one of the stacked 3HS2 is also reported. It shows a well-defined local and global structure defined by an extensive set of classical NMR restraints and residual dipolar couplings. Analysis of its global conformation and that of other representatives of the 3H family, shows that the relative orientations of the stacked and non-stacked arms, are restricted to narrow regions of conformational space, which can be understood from geometric considerations. Together, these findings open up the possibility of full prediction of 3HS2 conformation (stacking and global fold) directly from sequence.
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(as it appears on PubMed at http://www.pubmed.gov), where 15199171 is the PubMed ID number.
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{{ABSTRACT_PUBMED_15199171}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SNJ OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SNJ OCA].
==Reference==
==Reference==
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[[Category: Residual dipolar coupling]]
[[Category: Residual dipolar coupling]]
[[Category: Three-way junction]]
[[Category: Three-way junction]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 08:55:25 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:35:40 2008''

Revision as of 03:35, 29 July 2008

Image:1snj.png

Template:STRUCTURE 1snj

Solution structure of the DNA three-way junction with the A/C-stacked conformation

Template:ABSTRACT PUBMED 15199171

About this Structure

Full experimental information is available from OCA.

Reference

Global structure of a DNA three-way junction by solution NMR: towards prediction of 3H fold., Wu B, Girard F, van Buuren B, Schleucher J, Tessari M, Wijmenga S, Nucleic Acids Res. 2004 Jun 15;32(10):3228-39. Print 2004. PMID:15199171

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