175d: Difference between revisions

Revision as of 12:38, 21 February 2008

THE DNA SEQUENCE GCGAATGAGC CONTAINING THE HUMAN CENTROMERE CORE SEQUENCE GAAT FORMS A SELF-COMPLEMENTARY DUPLEX WITH SHEARED G:A PAIRS IN SOLUTION

OverviewOverview

The DNA sequence dGCGAATGAGC has a well-resolved, two-dimensional nuclear Overhauser (NOESY) spectrum that is suitable for high quality solution structure determination by NMR methods; in solution this sequence forms a stable self-complementary duplex containing sheared G.A base-pairs. A total of 220 distance constraints derived from time-dependent NOE measurements were collected and refined by repeated back-calculation of the NOESY spectra. Distance information from imino proton studies and from exclusive two-dimensional correlated spectroscopy (E. COSY) and/or linewidth analysis was included in the structure calculation using the program DSPACE 4.2, followed by restrained energy minimization with the program DISCOVER using the AMBER force field. The energies of the distance geometry (DG) structures decreased rapidly in the first few cycles and approached -510 +/- 3 kcal after 1000 cycles of conjugate gradient minimization (about 540 kcal lower than in the initial DG structures). All 15 final DG structures converged to a single family of closely related structures with pair-wise r.m.s.d. values of 0.96 +/- 0.34 A, which was further reduced by energy minimization to 0.70 +/- 0.35 A. Rather unusual structural features of the duplex are revealed in the final structures. The results indicate that, in addition to normal sequences with standard base-pairing, unusual nucleic acid structures can also be determined in solution with quite high precision by NMR/distance geometry methods.

About this StructureAbout this Structure

175D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

ReferenceReference

DNA sequence GCGAATGAGC containing the human centromere core sequence GAAT forms a self-complementary duplex with sheared G.A pairs in solution., Chou SH, Cheng JW, Fedoroff O, Reid BR, J Mol Biol. 1994 Aug 19;241(3):467-79. PMID:8064859

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OCA

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 '''THE DNA SEQUENCE GCGAATGAGC CONTAINING THE HUMAN CENTROMERE CORE SEQUENCE GAAT FORMS A SELF-COMPLEMENTARY DUPLEX WITH SHEARED G:A PAIRS IN SOLUTION'''<br />
 ==Overview==
-The DNA sequence dGCGAATGAGC has a well-resolved, two-dimensional nuclear, Overhauser (NOESY) spectrum that is suitable for high quality solution, structure determination by NMR methods; in solution this sequence forms a, stable self-complementary duplex containing sheared G.A base-pairs. A, total of 220 distance constraints derived from time-dependent NOE, measurements were collected and refined by repeated back-calculation of, the NOESY spectra. Distance information from imino proton studies and from, exclusive two-dimensional correlated spectroscopy (E. COSY) and/or, linewidth analysis was included in the structure calculation using the, program DSPACE 4.2, followed by restrained energy minimization with the, program DISCOVER using the AMBER force field. The energies of the distance, geometry (DG) structures decreased rapidly in the first few cycles and, approached -510 +/- 3 kcal after 1000 cycles of conjugate gradient, minimization (about 540 kcal lower than in the initial DG structures). All, 15 final DG structures converged to a single family of closely related, structures with pair-wise r.m.s.d. values of 0.96 +/- 0.34 A, which was, further reduced by energy minimization to 0.70 +/- 0.35 A. Rather unusual, structural features of the duplex are revealed in the final structures., The results indicate that, in addition to normal sequences with standard, base-pairing, unusual nucleic acid structures can also be determined in, solution with quite high precision by NMR/distance geometry methods.
+The DNA sequence dGCGAATGAGC has a well-resolved, two-dimensional nuclear Overhauser (NOESY) spectrum that is suitable for high quality solution structure determination by NMR methods; in solution this sequence forms a stable self-complementary duplex containing sheared G.A base-pairs. A total of 220 distance constraints derived from time-dependent NOE measurements were collected and refined by repeated back-calculation of the NOESY spectra. Distance information from imino proton studies and from exclusive two-dimensional correlated spectroscopy (E. COSY) and/or linewidth analysis was included in the structure calculation using the program DSPACE 4.2, followed by restrained energy minimization with the program DISCOVER using the AMBER force field. The energies of the distance geometry (DG) structures decreased rapidly in the first few cycles and approached -510 +/- 3 kcal after 1000 cycles of conjugate gradient minimization (about 540 kcal lower than in the initial DG structures). All 15 final DG structures converged to a single family of closely related structures with pair-wise r.m.s.d. values of 0.96 +/- 0.34 A, which was further reduced by energy minimization to 0.70 +/- 0.35 A. Rather unusual structural features of the duplex are revealed in the final structures. The results indicate that, in addition to normal sequences with standard base-pairing, unusual nucleic acid structures can also be determined in solution with quite high precision by NMR/distance geometry methods.
 ==About this Structure==
-D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=175D OCA].
+D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=175D OCA].
 ==Reference==
 DNA sequence GCGAATGAGC containing the human centromere core sequence GAAT forms a self-complementary duplex with sheared G.A pairs in solution., Chou SH, Cheng JW, Fedoroff O, Reid BR, J Mol Biol. 1994 Aug 19;241(3):467-79. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8064859 8064859]
 [[Category: Protein complex]]
-[[Category: Cheng, J.W.]]
+[[Category: Cheng, J W.]]
-[[Category: Chou, S.H.]]
+[[Category: Chou, S H.]]
 [[Category: Fedoroff, O.]]
-[[Category: Reid, B.R.]]
+[[Category: Reid, B R.]]
 [[Category: dna]]
 [[Category: double helix]]
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 [[Category: sheared g:a pairs]]
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