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132d

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{{STRUCTURE_132d| PDB=132d | SCENE= }}
{{STRUCTURE_132d| PDB=132d | SCENE= }}
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'''SOLUTION STRUCTURE OF THE TN AN DNA DUPLEX GCCGTTAACGGC CONTAINING THE HPA I RESTRICTION SITE'''
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===SOLUTION STRUCTURE OF THE TN AN DNA DUPLEX GCCGTTAACGGC CONTAINING THE HPA I RESTRICTION SITE===
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==Overview==
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The solution structure of the self-complementary DNA duplex [d(GCCGTTAACGGC)]2, which contains the HpaI restriction site GTTAAC, has been elucidated by two-dimensional NMR, distance geometry (DG), and NOE back-calculation methods. Initial distance constraints were determined by polynomial fitting the two-spin initial NOE rates; backbone constraints from NOE and J-coupling observations (Kim et al., 1992) were included. RMSDs between initial-distance-refined structures derived from random-embedded DG, A-DNA, and B-DNA starting structures were all in the range 0.5-1.0 A, indicating good convergence properties of the algorithm, regardless of the starting structure. A semiautomatic back-calculation refinement procedure was developed and used to generate more refined structures for which the BKCALC-simulated NOE volumes matched the experimental data. The six final structures refined from various starting structures exhibit very good agreement with the experimental data (R values = 0.18) and converge well to within 0.8-A RMSD differences for the central 8 base pairs. The torsion and pseudorotation phase angles were found to be well determined by the data, and the local helical parameters for each base step converged quite well. The final structures show that the central T6-A7 step is somewhat underwound (twist angle ca. 29 degrees), with a large negative cup and a normal (wide) minor groove width, while the T5-T6 and A7-A8 steps have a partially narrowed minor groove.
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(as it appears on PubMed at http://www.pubmed.gov), where 1457407 is the PubMed ID number.
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{{ABSTRACT_PUBMED_1457407}}
==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=132D OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=132D OCA].
==Reference==
==Reference==
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[[Category: Double helix]]
[[Category: Double helix]]
[[Category: Hpa 1 restriction site]]
[[Category: Hpa 1 restriction site]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:28:50 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 15:27:27 2008''

Revision as of 12:27, 30 June 2008

Image:132d.png

Template:STRUCTURE 132d

SOLUTION STRUCTURE OF THE TN AN DNA DUPLEX GCCGTTAACGGC CONTAINING THE HPA I RESTRICTION SITE

Template:ABSTRACT PUBMED 1457407

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure of the TnAn DNA duplex GCCGTTAACGCG containing the HpaI restriction site., Kim SG, Reid BR, Biochemistry. 1992 Dec 8;31(48):12103-16. PMID:1457407

Page seeded by OCA on Mon Jun 30 15:27:27 2008

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