2dd3

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{{STRUCTURE_2dd3| PDB=2dd3 | SCENE= }}
{{STRUCTURE_2dd3| PDB=2dd3 | SCENE= }}
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'''An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack'''
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===An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack===
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==Overview==
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A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA pair). An unusually stable loop with three consecutive sheared GA pairs forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts with that reported for this loop in the crystal structure of the large ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in alternative base stacking and pseudosymmetry with exclusively sheared pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.
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(as it appears on PubMed at http://www.pubmed.gov), where 16734425 is the PubMed ID number.
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{{ABSTRACT_PUBMED_16734425}}
==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=2DD3 OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD3 OCA].
==Reference==
==Reference==
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[[Category: Sequence specific a-minor motif]]
[[Category: Sequence specific a-minor motif]]
[[Category: Thermodynamic]]
[[Category: Thermodynamic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 00:11:59 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:13:42 2008''

Revision as of 00:13, 29 July 2008

Image:2dd3.png

Template:STRUCTURE 2dd3

An alternating sheared AA pair in 5'GGUGAAGGCU/3'PCCGAAGCCG: II. The minor conformation with A6/A5/A16 stack

Template:ABSTRACT PUBMED 16734425

About this Structure

Full experimental information is available from OCA.

Reference

An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA., Chen G, Kennedy SD, Qiao J, Krugh TR, Turner DH, Biochemistry. 2006 Jun 6;45(22):6889-903. PMID:16734425

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