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231d

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{{STRUCTURE_231d| PDB=231d | SCENE= }}
{{STRUCTURE_231d| PDB=231d | SCENE= }}
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'''STRUCTURE OF A DNA-PORPHYRIN COMPLEX'''
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===STRUCTURE OF A DNA-PORPHYRIN COMPLEX===
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==Overview==
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We report the 2.4 A resolution X-ray structure of a complex in which a small molecule flips a base out of a DNA helical stack. The small molecule is a metalloporphyrin, CuTMPyP4 [copper(II) meso-tetra(N-methyl-4-pyridyl)porphyrin], and the DNA is a hexamer duplex, [d(CGATCG)]2. The porphyrin system, with the copper atom near the helical axis, is located within the helical stack. The porphyrin binds by normal intercalation between the C and G of 5' TCG 3' and by extruding the C of 5' CGA 3'. The DNA forms a distorted right-handed helix with only four normal cross-strand Watson-Crick base pairs. Two pyridyl rings are located in each groove of the DNA. The complex appears to be extensively stabilized by electrostatic interactions between positively charged nitrogen atoms of the pyridyl rings and negatively charged phosphate oxygen atoms of the DNA. Favorable electrostatic interactions appear to draw the porphyrin into the duplex interior, offsetting unfavorable steric clashes between the pyridyl rings and the DNA backbone. These pyridyl-backbone clashes extend the DNA along its axis and preclude formation of van der Waals stacking contacts in the interior of the complex. Stacking contacts are the primary contributor to stability of DNA. The unusual lack of van der Waals stacking contacts in the porphyrin complex destabilizes the DNA duplex and decreases the energetic cost of local melting. Thus extrusion of a base appears to be facilitated by pyridyl-DNA steric clashes.
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{{ABSTRACT_PUBMED_8608116}}
==About this Structure==
==About this Structure==
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[[Category: Flipped-out base]]
[[Category: Flipped-out base]]
[[Category: Right handed dna]]
[[Category: Right handed dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:20:54 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 11:29:44 2008''

Revision as of 08:29, 28 July 2008

Image:231d.png

Template:STRUCTURE 231d

STRUCTURE OF A DNA-PORPHYRIN COMPLEX

Template:ABSTRACT PUBMED 8608116

About this Structure

Full crystallographic information is available from OCA.

Reference

Structure of DNA-porphyrin complex., Lipscomb LA, Zhou FX, Presnell SR, Woo RJ, Peek ME, Plaskon RR, Williams LD, Biochemistry. 1996 Mar 5;35(9):2818-23. PMID:8608116

Page seeded by OCA on Mon Jul 28 11:29:44 2008

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