[21] Induced structural changes in protein-DNA complexes

Two Structures of a λ Cro Variant Highlight Dimer Flexibility but Disfavor Major Dimer Distortions upon Specific Binding of Cognate DNA

“…Direct NMR comparisons of bound and unbound λ Cro by Kyogoku et al 23 have been interpreted to suggest some induced-fit changes in protein structure upon binding to the O R 3 site. In particular, DNA-induced changes have been observed in backbone 15 N and 1 H chemical shifts 23 and methyl 1 H shifts 24 in the region of residues 40-53, which includes strand β2 and part of β3 but does not directly contact DNA.…”

“…In particular, DNA-induced changes have been observed in backbone 15 N and 1 H chemical shifts 23 and methyl 1 H shifts 24 in the region of residues 40-53, which includes strand β2 and part of β3 but does not directly contact DNA. The direction of the changes in backbone shifts was interpreted to suggest that the β2-β3 strand interaction tightens upon DNA complexation, while the β1-β2 interaction loosens.…”

“…The direction of the changes in backbone shifts was interpreted to suggest that the β2-β3 strand interaction tightens upon DNA complexation, while the β1-β2 interaction loosens. 23 Chemical shift changes in the region of residues 54-56 were also interpreted as indicative of a strengthened intermolecular β-sheet at the end of the β3 strand, 23 although residues in this region also make direct contacts to the DNA backbone 14 and could be perturbed by these interactions rather than by changes in protein structure. Within the same region, the photochemically induced dynamic nuclear polarization behavior of Tyr51 is also affected by specific DNA binding to O R 3.…”

DNA Duplex Dynamics: NMR Relaxation Studies of a Decamer with Uniformly13C-Labeled Purine Nucleotides

“…The labeled nucleoside was chemically converted to the 2Ј-deoxy form (47) and subsequently its 3Ј-phosphoramidite (48), which was used for oligonucleotide synthesis on a DNA synthesizer (Applied Biosystems Inc., ABI 392). The two fully protected and labeled DNA strands, d(CATTTG-CATC) and d(GATGCAAATG), were deblocked and purified by the conventional C18 HPLC column procedure (49). Every purine was enriched with 13 C and 15 N, but pyrimidines were not.…”

New Sequential‐Assignment Routes of Nucleic Acid NMR Signals Using a [5′‐13C]‐Labeled DNA Dodecamer

“…[7 -9] These were used for the construction of 5'-d(* 1 C* 2 G* 3 C* 4 G* 5 A* 6 A* 7 T* 8 T* 9 C* 10 G* 11 C 12 G)-3' by the solid-phase phosphoramidite method [10] using G-CPG at the 3' terminus. [11] All 1 H and 31 P assignments for this oligomer at 30°C have been reported by Hare and co-workers, [12] Kellogg and Schweitzer, [13] and Ono and co-workers. Purification of the oligonucleotide was performed according to the method of Kyogoku and coworkers.…”