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| | {{STRUCTURE_231d| PDB=231d | SCENE= }} | | {{STRUCTURE_231d| PDB=231d | SCENE= }} |
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| - | '''STRUCTURE OF A DNA-PORPHYRIN COMPLEX'''
| + | ===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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_8608116}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 8608116 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_8608116}} |
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| | ==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]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:20:54 2008'' | + | |
| | + | ''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
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
