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==SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE== | |||
<StructureSection load='1aul' size='340' side='right'caption='[[1aul]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1aul]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AUL FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THX:PHOSPHONIC+ACID+6-({6-[6-(6-CARBAMOYL-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONYL)-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDOCENE-2-CARBONYL]-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONL}-AMINO)-HEXYL+ESTER+5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL+ESTER'>THX</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1aul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aul OCA], [https://pdbe.org/1aul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1aul RCSB], [https://www.ebi.ac.uk/pdbsum/1aul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1aul ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
== | |||
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. | 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. | ||
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<ref>PMID:9443977</ref> | |||
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 | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1aul" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Foti M]] | |||
[[Category: Gamper Junior HB]] | |||
[[Category: Gorn VV]] | |||
[[Category: Kumar S]] | |||
[[Category: Lukhtanov EA]] | |||
[[Category: Meyer Junior RB]] | |||
[[Category: Reed MW]] | |||
[[Category: Schweitzer BI]] | |||
[[Category: West J]] | |||
Latest revision as of 14:33, 22 November 2023
SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURESOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE
Structural highlights
Publication Abstract from PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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