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2oey

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{{STRUCTURE_2oey| PDB=2oey | SCENE= }}
{{STRUCTURE_2oey| PDB=2oey | SCENE= }}
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'''Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA'''
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===Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA===
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==Overview==
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The solution structure of the complex formed between an oligodeoxynucleotide containing a two-base bulge (5'-CCATCGTCTACCTTTGGTAGGATGG) and SCA-alpha2, a designed spirocyclic helical molecule, has been elucidated. SCA-alpha2, a close mimic of the metabolite, NCSi-gb, of the DNA bulge-specific enediyne antibiotic neocarzinostatin, differs in possessing a more stable spirocyclic ring system and in lacking certain bulky groupings that compromise bulged DNA binding. This study provides a detailed comparison of the binding modes of the two complexes and provides new insights into the importance of shape and space, as opposed to simple nucleotide sequence, in complex formation at the bulge site. The two rigidly held aromatic rings of SCA-alpha2 form a right-handed helical molecular wedge that specifically penetrates the bulge-binding pocket and immobilizes the two bulge residues (GT), which point toward the minor groove, rather than the major groove as in the NCSi-gb.bulged DNA complex. The ligand aromatic ring systems stack on the DNA bulge-flanking base pairs that define the long sides of the triangular prism binding pocket. Like NCSi-gb, SCA-alpha2 possesses the natural N-methylfuranose moiety, alpha-linked to the benzindanol (BI) moiety. The amino sugar anchors in the major groove of the DNA and points toward the 3'-bulge-flanking base pair. Lacking the bulky cyclocarbonate of NCSi-gb, the SCA-alpha2.bulged DNA complex has a much less twisted and buckled 3'-bulge-flanking base pair (dG20.dC8), and the G20 residue stacks directly above the BI ring platform. Also, the absence of the methyl group and the free rotation of the methoxy group on the dihydronaphthanone (NA) moiety of SCA-alpha2 allow better stacking geometry of the NA ring above the 5'-bulge-flanking dG21.dC5 base pair. These and other considerations help to explain why NCSi-gb binds very poorly to bulged RNA and are consistent with the recent observation of good binding with SCA-alpha2. Thus, although the two complexes resemble each other closely, they differ in important local environmental details. SCA-alpha2 has a better hand-in-glove fit at the bulge site, making it an ideal platform for the placement of moieties that can react covalently with the DNA and for generating congeners specific for bulges in RNA.
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(as it appears on PubMed at http://www.pubmed.gov), where 17388570 is the PubMed ID number.
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{{ABSTRACT_PUBMED_17388570}}
==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=2OEY OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA].
==Reference==
==Reference==
Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA., Zhang N, Lin Y, Xiao Z, Jones GB, Goldberg IH, Biochemistry. 2007 Apr 24;46(16):4793-803. Epub 2007 Mar 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17388570 17388570]
Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA., Zhang N, Lin Y, Xiao Z, Jones GB, Goldberg IH, Biochemistry. 2007 Apr 24;46(16):4793-803. Epub 2007 Mar 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17388570 17388570]
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Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analog., Stassinopoulos A, Ji J, Gao X, Goldberg IH, Science. 1996 Jun 28;272(5270):1943-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8658168 8658168]
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Induced formation of a DNA bulge structure by a molecular wedge ligand-postactivated neocarzinostatin chromophore., Gao X, Stassinopoulos A, Ji J, Kwon Y, Bare S, Goldberg IH, Biochemistry. 2002 Apr 23;41(16):5131-43. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11955061 11955061]
[[Category: Goldberg, I H.]]
[[Category: Goldberg, I H.]]
[[Category: Jones, G B.]]
[[Category: Jones, G B.]]
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[[Category: Zhang, N.]]
[[Category: Zhang, N.]]
[[Category: Designed spirocyclic helical ligand-bulged dna complex]]
[[Category: Designed spirocyclic helical ligand-bulged dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 10:45:56 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 09:32:16 2008''

Revision as of 06:32, 28 July 2008

Image:2oey.png

Template:STRUCTURE 2oey

Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA

Template:ABSTRACT PUBMED 17388570

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA., Zhang N, Lin Y, Xiao Z, Jones GB, Goldberg IH, Biochemistry. 2007 Apr 24;46(16):4793-803. Epub 2007 Mar 28. PMID:17388570

Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analog., Stassinopoulos A, Ji J, Gao X, Goldberg IH, Science. 1996 Jun 28;272(5270):1943-6. PMID:8658168

Induced formation of a DNA bulge structure by a molecular wedge ligand-postactivated neocarzinostatin chromophore., Gao X, Stassinopoulos A, Ji J, Kwon Y, Bare S, Goldberg IH, Biochemistry. 2002 Apr 23;41(16):5131-43. PMID:11955061

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