Transcription factor 1 (TF1), encoded by the Bacillus subtilis bacteriophage SPO1, is a DNA-binding protein of the HU family. In preparation for a determination of the structure of the DNA-TF1 complex, we have studied the conformation of one core 17-mer duplex d(5'-CACTACTCTTTGTAGTG-3')-d(5'-CACTACAAAGAGTAGTG-3'). NOESY, DQF-COSY and TOCSY spectroscopy provide resonance assignments of non-exchangeable and exchangeable protons, internucleotide and interstrand proton-proton distances, and dihedral angle constraints. Restrained molecular dynamics calculations yield a family of NMR solution structures for which the RMSD is 0.7 A (all atoms). The helical twist is 34.9 degrees for the central 15 bp. Bends toward the major groove are located between the second and fourth base pairs from each end. The G12 x C23 base pair, which is bounded on each side by consecutive A x T pairs, causes a local disturbance to the DNA helix that makes the conformations of the two end segments unsymmetrical. The pyrimidine rings at T9, T10 and T11 experience more extensive rotational movement than the rest of the structure.
[NMR paper] NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II
NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II) d(GpG) intrastrand cross-link, the major adduct of the anticancer drug cisplatin.
Related Articles NMR solution structure of a DNA dodecamer duplex containing a cis-diammineplatinum(II) d(GpG) intrastrand cross-link, the major adduct of the anticancer drug cisplatin.
Biochemistry. 1998 Jun 30;37(26):9230-9
Authors: Gelasco A, Lippard SJ
The structure of the DNA duplex dodecamer, d(CCTCTGGTCTCC. GGAGACCAGAGG), containing the cisplatin d(GpG) 1,2-intrastrand...
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NMR study of hydrogen exchange during the B-Z transition of a DNA duplex induced by t
NMR study of hydrogen exchange during the B-Z transition of a DNA duplex induced by the Z? domains of yatapoxvirus E3L.
Related Articles NMR study of hydrogen exchange during the B-Z transition of a DNA duplex induced by the Z? domains of yatapoxvirus E3L.
FEBS Lett. 2010 Oct 8;
Authors: Lee EH, Seo YJ, Ahn HC, Kang YM, Kim HE, Lee YM, Choi BS, Lee JH
The Yaba-like disease viruses (YLDV) are members of the Yatapoxvirus family and have double-stranded DNA genomes. The E3L protein, which is essential for pathogenesis in the vaccinia virus,...
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[NMR paper] 31P NMR spectra of oligodeoxyribonucleotide duplex lac operator-repressor headpiece c
31P NMR spectra of oligodeoxyribonucleotide duplex lac operator-repressor headpiece complexes: importance of phosphate ester backbone flexibility in protein-DNA recognition.
Related Articles 31P NMR spectra of oligodeoxyribonucleotide duplex lac operator-repressor headpiece complexes: importance of phosphate ester backbone flexibility in protein-DNA recognition.
Biochemistry. 1992 Feb 18;31(6):1849-58
Authors: Karslake C, Botuyan MV, Gorenstein DG
The 31P NMR spectra of various 14-base-pair lac operators bound to both wild-type and mutant lac...
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[NMR paper] 31P NMR spectra of an oligodeoxyribonucleotide duplex lac operator-repressor headpiec
31P NMR spectra of an oligodeoxyribonucleotide duplex lac operator-repressor headpiece complex.
Related Articles 31P NMR spectra of an oligodeoxyribonucleotide duplex lac operator-repressor headpiece complex.
Biochemistry. 1990 Jul 17;29(28):6578-84
Authors: Karslake C, Schroeder S, Wang PL, Gorenstein DG
The interaction of a symmetric lac operator duplex, d(TGTGAGCGCTCACA)2, with the N-terminal 56-residue headpiece fragment of the lac repressor protein was monitored by 31P NMR spectroscopy. The changes in the 31P chemical shifts upon addition...
1H NMR studies of a 17-mer DNA duplex.
Linear Mode
