Salt-dependent binding of Escherichia coli initiation factor 3 to nucleic acids determined by sedimentation partition chromatography.

The binding of 14CH3- initiation factor 3 (IF3) to polynucleotides is strongly dependent upon the concentration of added salt. The observed association constant, Kobs, increases by ca. a factor of 10(2) when the NaCl concentration is lowered from 200 to 100 mM for the binding of 14CH3-IF3 to all nucleic acids examined. This salt-dependent binding suggests that at physiological salt concentrations the formation of an IF3-polynucleotide complex is primarily driven by the release of cations from the nucleic acid, although anion effects are involved also. For single-stranded nucleic acids, nonelectrostatic interactions may contribute a factor of 10(2) to the value of Kobs, although accurate assessment of these interactions is complicated by anion effects. The binding of 14CH3-IF3 to the double helix, poly(A).poly(U), appears to be exclusively electrostatic. 14CH3-IF3 forms a maximum of 8 +/- 2 ion pairs with most single-stranded polynucleotides. The value of Kobs increases from ca. 10(3) to 10(5) M-1 when the NaCl concentration is lowered from 200 to 100 mM for the binding of 14CH3-IF3 to poly(A), poly(C), poly(U), and poly(A).poly(U). At physiological salt concentrations, IF3 shows no preference for any of these bases or for single or double-stranded structures. However, 14CH3-IF3 binds ca. 60 times greater to poly(A,G), at al NaCl concentrations examined, than to the other nucleic acids, indicating that IF3 has some preference for guanine-containing polynucleotides. The presence of 10 mM Mg2+ tends to reduce the value of Kobs at any given NaCl concentration, but to a smaller degree than predicted by simply a competition between Mg2+ and IF3 for the nucleic acid lattice.

Circular dichroism study of Escherichia coli initiation factor 3 binding to nucleic acids.

The circular dichroic spectral features of (A)10-20, (C)10-20, A8UGU6, poly(A), and poly(C), at both neutral and acidic pH values and in the presence and absence of Mg2+, are significantly altered by Escherichia coli initiation factor 3 (IF3), implying the occurrence of protein-induced changes in nucleic acid secondary structure. Similarly, the circular dichroic spectral characteristics of helical poly(U), poly-(A)-poly(U), and poly(I)-poly(C) are modified by IF3. However, no structural perturbation of poly(A)-poly(U) occurs in the absence of Mg2+ by IF3. The oligonucleotides (A)10-20 and (C)10-20 at both pH 7.5 and 5.5 titrate to end point of 26 +/- 4 nucleotide residues per IF3 [except (C) 10-20 at pH 5.5 which titrates to 17 +/- 1 nucleotide residues per IF3], whereas the hairpin A8UGU6 under similar conditions at neutral pH and in the presence of Mg2+ titrates to an end point of 56 +/- 3 nucleotide residues per IF3, thereby suggesting the presence of multiple binding sites on the protein. By contrast, poly(A) and poly(C) at neutral pH and in the absence of Mg2+ titrate to an end point of 13 +/- 1 nucleotide residues per IF3. The occurrence of significant light-scattering artifacts precluded a determination of the end point stoichiometry in most other cases. The circular dichroic spectra of E. coli tRNA, MS2 RNA, phiX174 DNA, and sonicated calf thymus DNA were unaffected by IF3 at physiological concentrations. Addition of an equimolar mixture of IF3 and ribosomal protein S1 titrates the circular dichroism of poly(C) at acid pH as did S1 alone. However, addition of IF3 to mixture of poly(A) and S1 at neutral pH did not result in significant titration of the optical activity until IF3 was in excess over S1, even though filter binding assays indicate normal IF3 binding to the polynucleotide. The possible relation of these observations to the biological function of IF3 is briefly considered.

A circular dichroism study of Escherichia coli Initiation Factor-1 binding to polynucleotides.

Binding of Escherichia coli Initiation Factor-1 protein to the nucleic acid lattice induces alterations in the secondary structures of a variety of purine and pyrimidine containing polynucleotides in both the single and double stranded conformations, as assessed by circular dichroism spectroscopy. The helical hairpin form of poly(U), the single-stranded stacked form of poly(C), and the duplex poly(A) x poly(U) (in the presence of Mg2+) are stoichiometrically converted by Initiation Factor-1 (IF-1) to structures spectrally indistinguishable from their partially or completely thermally denatured forms. By contrast, the binding of IF-1 to double stranded poly(C), single- and double-stranded poly(A) elicited spectral responses which were interpreted in terms of diminished base-base interaction, not equivalent to that induced by thermal means. Stoichiometric endpoints of 3-5 nucleotide residues/IF-1 were determined for polynucleotide structures in those cases where light scattering artifacts at low nucleotide residue to protein ratios were absent. In the absence of Mg2+ IF-1 was unable to elicit a conformation alteration effect in poly(A) x poly(U), while for poly(U) much less of an effect was observed than in the presence of this divalent ion. The functional significance of these results is briefly considered.