1aul

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[[Image:1aul.gif|left|200px]]
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{{Seed}}
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{{STRUCTURE_1aul| PDB=1aul | SCENE= }}
{{STRUCTURE_1aul| PDB=1aul | SCENE= }}
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'''SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE'''
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===SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE===
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==Overview==
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The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions.
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The line below this paragraph, {{ABSTRACT_PUBMED_9443977}}, adds the Publication Abstract to the page
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(as it appears on PubMed at http://www.pubmed.gov), where 9443977 is the PubMed ID number.
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{{ABSTRACT_PUBMED_9443977}}
==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=1AUL OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AUL OCA].
==Reference==
==Reference==
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[[Category: Cdpi3]]
[[Category: Cdpi3]]
[[Category: Deoxyribonucleic acid]]
[[Category: Deoxyribonucleic acid]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 10:42:28 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 17:37:13 2008''

Revision as of 14:37, 30 June 2008

Image:1aul.png

Template:STRUCTURE 1aul

SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE

Template:ABSTRACT PUBMED 9443977

About this Structure

Full experimental information is available from OCA.

Reference

Solution structure of a highly stable DNA duplex conjugated to a minor groove binder., Kumar S, Reed MW, Gamper HB Jr, Gorn VV, Lukhtanov EA, Foti M, West J, Meyer RB Jr, Schweitzer BI, Nucleic Acids Res. 1998 Feb 1;26(3):831-8. PMID:9443977

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