Molecular Dynamics in Protein—Single Stranded DNA Complexes. Two Distinct Nucleoside Mobilities in Poly(deoxythymidylic acid)—Gene 5 Protein Complexes

Kao, Shih-Chung; Bobst, Elisabeth V.; Pauly, Gary T.; Bobst, Albert M.

doi:10.1080/07391102.1985.10508415

Cited by 5 publications

(2 citation statements)

References 13 publications

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“…At the limit, this type of interaction may come to resemble the dsDNA binding reported by Sang and Gray (1987). ESR experiments of the type performed by Kao et al (1985) could help resolve this question. Secondly, EM studies on G5P-fdDNA complexes (Gray, 1985) suggest that an = 3 complex has approximately 15% more superhelical turns and approximately 15% more nucleotides per turn than an = 4 complex, rather than the 30% more turns predicted.…”

Section: Discussionmentioning

confidence: 80%

“…NOE data for the G5Pd(pA)4 complex have been interpreted in terms of the enclosure of two bases by the "clamp" (King & Coleman, 1987) but could be equally consistent with a single-base enclosure. Support for a one-base site comes from ESR studies of G5P binding to spin-labeled poly(dT), which concluded that only one of four bases within the DNA binding channel was strongly immobilized (Kao et al, 1985). The Ade H2 chemical shift behavior (Table I) suggests that substantial destacking of adenine bases occurs upon binding.…”

Section: Discussionmentioning

confidence: 99%

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Ff gene 5 protein-d(pA)40-60 complex: proton NMR supports a localized base-binding model

King¹,

Coleman²

1988

Biochemistry

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The interaction between Ff gene 5 protein (G5P) and d(pA)40-60 serves as an improved model system for a 1H NMR examination of the G5P-ssDNA interface under cooperative binding conditions. Selective deuteriation of aromatic residues enables individual Tyr (3,5)H and (2,6)H resonances to be monitored in spectra of high molecular weight nucleoprotein assemblies. Analysis of complexation-induced chemical shift changes and intermolecular NOEs indicates that Tyr 26 is the only tyrosine to interact directly with ssDNA. Tyr 41, which is immobilized upon binding, is implicated in a dimer-dimer contact role. These and other NMR data are consistent with a previously outlined model of the protein-DNA interface in which Phe 73', Leu 28, and Tyr 26 form components of a base-binding pocket or "dynamic clamp" fringed by a cluster of positively charged residues [King, G. C., & Coleman, J. E. (1987) Biochemistry 26, 2929-2937]. In the present version of this model, the Phe and Leu side chains are proposed to stack on either side of a single base, while there is the possibility that Tyr 26 may H-bond to the sugar-phosphate backbone in addition to or instead of stacking. Chemical-exchange effects underscore the dynamic nature of binding at the pocket. A comparison of d(pA)40-60 and oligo(dA)-induced chemical shift changes suggests that poly- and oligonucleotide complexes have indistinguishable base-binding loci but appear to differ in their dimer-dimer interactions.(ABSTRACT TRUNCATED AT 250 WORDS)

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Section: Discussionmentioning

confidence: 80%

Section: Discussionmentioning

confidence: 99%

Ff gene 5 protein-d(pA)40-60 complex: proton NMR supports a localized base-binding model

King¹,

Coleman²

1988

Biochemistry

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Nick translation of λ phage DNA with a deoxycytidine analog spin labeled in the 5 position

Strobel¹,

Bobst²,

Bobst³

1989

Archives of Biochemistry and Biophysics

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Redox-active daunomycin-spin-labeled nucleic acid complexes

Ireland¹,

Pauly²,

Bobst³

et al. 1986

Biochemistry

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Interaction studies between daunomycin (DM) and enzymatically spin-labeled nucleic acid duplexes reveal two modes of binding by electron spin resonance (ESR) spectroscopy. At a low drug/nucleotide (D/N) ratio, the drug binds in the intercalative mode with only a slight reduction in base mobility. Saturation in the intercalative mode is achieved at a lower D/N ratio for B' DNA than for B DNA. After full intercalation, further addition of DM seems to destabilize the helix and to allow the formation of redox-active DM stacks complexed to the nucleic acid lattice. These stacks will irreversibly oxidize all the nitroxides covalently bound to the 4- or 5-position of the pyrimidine base. Interactions between DM and spin-labeled single-stranded nucleic acids lead directly to the formation of redox-active complexes, while mixing of the drug with spin-labeled nucleic acid building blocks not incorporated in a nucleic acid lattice causes no ESR signal change. Complete disappearance of the ESR signal of spin-labeled nucleic acids extrapolates to a D/N value which is a constant for a particular lattice system and is independent of spin-labeling content.

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Molecular Dynamics in Protein—Single Stranded DNA Complexes. Two Distinct Nucleoside Mobilities in Poly(deoxythymidylic acid)—Gene 5 Protein Complexes

Cited by 5 publications

References 13 publications

Ff gene 5 protein-d(pA)40-60 complex: proton NMR supports a localized base-binding model

Ff gene 5 protein-d(pA)40-60 complex: proton NMR supports a localized base-binding model

Nick translation of λ phage DNA with a deoxycytidine analog spin labeled in the 5 position

Redox-active daunomycin-spin-labeled nucleic acid complexes

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