Nonspecific interaction of Escherichia coli pyrenyl RNA polymerase holoenzyme with synthetic polynucleotides as monitored by fluorescence spectroscopy

A derivative of RNA polymerase containing approximately 2 pyrene equiv per enzyme molecule has been used to study the interaction of RNA polymerase with poly[d(A-T)].poly[d(A-T)] and poly[d-(G-C)].poly[d(G-C)]. As monitored by fluorescence spectroscopy, pyrenyl RNA polymerase displays a unique set of conformational changes with each synthetic polynucleotide as a function of temperature. An increase in the fluorescence intensity was observed for both polynucleotides at 5 degrees C. A decrease was observed in the case of poly[d(A-T)].poly[d(A-T)] at 25 and 37 degrees C, whereas no discernible perturbation was observed in the case of poly[d(G-C)].poly[d(G-C)]. Different salt dependencies were observed for the interaction of pyrenyl RNA polymerase with these polynucleotides at 5 and 25 degrees C. Further characterization of these interactions as well as correlation of the observed fluorescence changes to the corresponding open and closed complexes was carried out with heparin. The interaction between pyrenyl RNA polymerase and poly[d-(A-T)].poly[d(A-T)] at 25 degrees C was quantified by using two different methods.(ABSTRACT TRUNCATED AT 250 WORDS)     

Right- and left-handed helixes of poly[d(A-T)].poly[d(A-T)] investigated by infrared spectroscopy

The secondary structures of double-stranded poly[d(A-T)].poly[d(A-T)] in films have been studied by IR spectroscopy with three different counterions (Na+, Cs+, and Ni2+) and a wide variety of water content conditions (relative humidity between 100 and 47%). In addition to the A-, B-, C-, and D-form spectra, a new IR spectrum has been obtained in the presence of nickel ions. The IR spectra of Ni2+-poly[d(A-T)].poly[d(A-T)] films are analyzed by comparison with previously assigned IR spectra of left-handed poly[d(G-C)].poly[d(G-C)] and poly[d(A-C)].poly[d(G-T)], and it is possible to conclude that they reflect a Z-type structure for poly[d(A-T)].poly[d(A-T)]. The Z conformation has been favored by the high polynucleotide concentration, by the low water content of the films, and by specific interactions of the transition metal ions with the purine bases stabilized in a syn conformation. A structuration of the water hydration molecules around the double-stranded Ni2+-poly[d(A-T)].poly[d(A-T)] is shown by the presence of a strong sharp water band at 1615 cm-1.     

Study of conformation characteristics of polydeoxyribonucleotides with non-random base sequence by slow 1H----3H exchange

The rate constants of 1H----3H exchange between water and C8H-groups of purinic residues of alternating polynucleotides: poly[d(A-T)].poly[d(A-T)] (I), poly[d(G-C)].poly[d(G-C)] (II), poly[d(A-C)].poly[d(G-T)] (III) and homopolynucleotides: poly(dA).poly(dt) (IV), poly(dG).poly(dC) (V), as well as DNA E. coli, was determined in 0.15 M NaCl at 25 degrees C. The retardation of exchange observed at these conditions (compared to that of the B-form DNA) is in agreement with the model of B-alternating structure for the (I) and is attributed to the co-existence of B- and A-conformers for the (V) in solution. Absence of distinguishable differences in exchange rate constants for purinic residues of the (II), (III) and (IV) (compared to that of the B-form DNA) evidences that conformations of these polynucleotides in solution are similar to "canonical" B-form DNA and don't correlate with the model of "heteronomous" DNA which was proposed for (IV).     

Template specificities of Aclacinomycin B on the inhibition of DNA-dependent RNA synthesis in vitro

Summary The effect of Aclacinomycin B (ACM-B), an anthracycline antitumor antibiotic, on the DNA-dependent RNA synthesis using single- and double-stranded DNAs of known base content and sequence is studied. The data show that ACM-B effectively inhibits the double-stranded DNA-directed RNA synthesis with a preference of poly[d(A-T)] > poly[d(G-C)] > poly[d(I-C)]. In contrast, it has no inhibitory effect on the template function of single-stranded DNA (e.g. poly dA, poly dT, and poly dC). These results suggest that the mechanism of ACM-13 inhibition, like other anthracycline antibiotics, is by intercalation. In addition to the base specificity, there are also dramatic differences in inhibition depending on the base sequence in the DNA template. Thus, ACM-13 preferentially inhibits the alternating double-stranded copolymers over the double-stranded homopolymers; e.g. poly [d(A-T)] is inhibited to a greater extent than poly dA · poly dT and poly [d(G-C)] is inhibited more than poly dG · poly dC. Since the inhibition by ACM-13 can be totally abolished when assayed in excess amount of DNA, this result suggests that ACM-B inhibition of RNA synthesis is solely on the DNA template (which is in support of the intercalation model), and has ruled out the possibility that ACM-B may also exert an inhibitory effect on the activity of RNA polymerase per se.     

Human 170 kDa and 180 kDa Topoisomerases II Bind Preferentially to Curved and Left-Handed Linear DNA

Abstract

The binding activities of the 170 kDa and the 180 kDa human topoisomerases II (topo IIa and topo IIβ) to linear DNA fragments with different degrees of curvature were characterized. In gel retardation experiments it was shown that both forms of the enzyme bind preferentially to a curved 287 bp fragment, forming a detectable stable complex. The affinity for straight DNA fragments of similar length is significantly lower. Both a commercially available topo IIa, isolated from placenta, and topo IIα and topo IIβ purified from nuclear extracts of the Namahva lymphoma tissue culture line gave similar results. The effects of double-stranded poly[d(A-T)], poly[d(G-C)], supercoiled plasmid DNA and linear Z-DNA on the topo II- complex with curved DNA were analyzed in competition experiments. The hierarchy of affinities of the 180 kDa topo IIβ for these DNAs has the order: linear left-handed DNA > supercoiled DNA ? curved DNA ? poly[d(A-T)] ? poly[d(G-C)]. The 170 kDa topo IIa binds with similar affinity to curved DNA and linear Z-DNA ? supercoiled DNA ? linear B- DNA The data imply that human topoisomerase II binding is more sensitive to DNA secondary structure than to DNA sequence per se. The ability of the enzyme to preferentially recognize a wide variety of sequences in unusual secondary structures suggests a mode of targeting the enzyme in vivo to regions of high negative supercoiling.     

Volume and hydration changes of DNA-ligand interactions

We report the volumetric and other thermodynamic properties of ethidium bromide (EB), propidium iodide (PI) and daunomycin (DAU) intercalating with poly(dA).poly(dT), poly[d(A-T)].poly[d(A-T)], and poly[d(G-C)].poly[d(G-C)], respectively, as well as minor groove binder Hoechst 33258 binding with poly[d(A-T)].poly[d(A-T)]. The data were obtained using fluorescence titration and hydrostatic pressure measurements. Our thermodynamic data are combined with enthalpies from literature reports to analyze the thermodynamic characteristics of the different interactions. The differences are interpreted based on three processes related to hydration: I. burial of non-polar hydrophobic solvent accessible surface, II. burial of polar surface and formation of solute-solute H-bonds, and III. disruption of "structural" hydration. Sequence dependent conformational changes may also be important when comparing ligand binding to different DNA sequences. We conclude that a combination of different thermodynamic parameters, especially volume change, is essential in order to understand the role of hydration in the energetics of DNA-ligand interactions.     

Direct measurement of the poliovirus RNA polymerase error frequency in vitro.

The fidelity of RNA replication by the poliovirus-RNA-dependent RNA polymerase was examined by copying homopolymeric RNA templates in vitro. The poliovirus RNA polymerase was extensively purified and used to copy poly(A), poly(C), or poly(I) templates with equimolar concentrations of noncomplementary and complementary ribonucleotides. The error frequency was expressed as the amount of a noncomplementary nucleotide incorporated divided by the total amount of complementary and noncomplementary nucleotide incorporated. The polymerase error frequencies were very high and ranged from 7 x 10(-4) to 5.4 x 10(-3), depending on the specific reaction conditions. There were no significant differences among the error frequencies obtained with different noncomplementary nucleotide substrates on a given template or between the values determined on two different templates for a specific noncomplementary substrate. The activity of the polymerase on poly(U) and poly(G) was too low to measure error frequencies on these templates. A fivefold increase in the error frequency was observed when the reaction conditions were changed from 3.0 mM Mg2+ (pH 7.0) to 7.0 mM Mg2+ (pH 8.0). This increase in the error frequency correlates with an eightfold increase in the elongation rate that was observed under the same conditions in a previous study.     

Highly selective affinity labeling of DNA-dependent RNA-polymerase II from human placenta

RNA polymerase II from human placenta was affinity labelled in crude preparation using two-step technique, which includes treatment of the enzyme with an aldehyde-containing reactive analogue of ATP, ADP or AMP in the presence of poly[d(A-T)] followed (after borohydride reduction) by the elongation of the attached label with [alpha-32P]UTP. A polypeptide of the molecular mass ca. 140 kDa proved to be the labelling target. No labelling was observed in the absence of poly[d(A-T)] or the reagent or in the presence of alpha-amanitin. All the results suggest the attachment of the affinity reagents to the second-largest subunit of the human RNA polymerase II, which therefore takes part in the initiation substrate's binding.     

Binding of meso-tetrakis(N-methylpyridiniumyl)porphyrin isomers to DNA: quantitative comparison of the influence of charge distribution and copper(II) derivatization

Factors influencing the binding of tetracationic porphyrin derivatives to DNA have been comprehensively evaluated by equilibrium dialysis, stopped-flow kinetics, etc., for mesotetrakis (4-N-methylpyridiniumyl)porphyrin [TMpyP (4)]. Technical difficulties have previously precluded a comprehensive study of metalloporphyrins. Since electrostatic interactions with the DNA and metal derivatization of the porphyrins have important consequences, we have investigated in greater detail two isomers of TMpyP (4) (meso-tetrakis(3-N-methylpyridiniumyl)porphyrin, [TMpyP (3)] and meso-tetrakis(2-N-methylpyridiniumyl)porphyrin [TMpyP (2)]) in which the position of the charged centers has been varied. A comprehensive study of the Cu(II) derivatives, e.g., CuTMpyP (4), was possible since the difficulties encountered previously with Ni(II) compounds were not a problem with Cu(II) porphyrins [J. A. Strickland, L. G. Marzilli, M. K. Gay, and W. D. Wilson (1988) Biochemistry 27, 8870-8878]. At 25 degrees C, the apparent equilibrium constants [Kobs] decreased with increasing [Na+] for all porphyrins. The Kobs values were comparable for TMpyP (4) and TMpyP (3) binding to either polyd(G-C).polyd(G-C) [poly[d(G-C)2]] or poly[d(A-T)].poly[d(A-T)] [poly[d(A-T)2]]. For the copper(II) porphyrins, the Kobs values were about fivefold greater. The Kobs value for CuTMpyP (2) binding to poly[d(G-C)2] was too small to measure under typical salt conditions; however, Kobs for binding to poly[d(A-T)2] was about two orders of magnitude smaller than those found for CuTMpyP (4) or CuTMpyP (3). Application of the condensation theory for polyelectrolytes suggests about three charge interactions when CuTMpyP (4), CuTMpyP (3), and TMpyP (3) bind to poly[d(G-C)2] or poly[d(A-T)2], a result comparable to that reported for TMpyP (4). At 20 degrees C and 0.115 M [Na+], incorporation of copper decreased the rates of dissociation from poly[d(A-T)2] by a 100-fold compared to those reported for TMpyP (4) but had little effect on the rates of dissociation from poly[d(G-C)2]. Also, movement of the H3CN+ group from the fourth to the third position of the pyridinium ring enhanced the rates of dissociation from poly[d(A-T)2] but decreased the rates of dissociation from poly[d(G-C)2]. From polyelectrolyte theory, the [Na+] dependence of the dissociation rates from poly[d(G-C)2] is consistent with intercalative binding, while that for poly[d(A-T)2] is consistent with an outside binding model. For calf thymus [CT] DNA at 20 degrees C, a greater decrease in the AT than in the GC imino 1H-nmr signal was observed upon addition of CuTMpyP (2), suggesting selective outside binding to the AT regions.(ABSTRACT TRUNCATED AT 400 WORDS)     

Mercury-induced transitions between right-handed and putative left-handed forms of poly[d(A-T).d(A-T)] and poly[d(G-C).d(G-C)]

Poly[d(A-T).d(A-T)] and poly[d(G-C).d(G-C)], each dissolved in 0.1 M NaClO4, 5 mM cacodylic acid buffer, pH 6.8, experience inversion of their circular dichroism (CD) spectrum subsequent to the addition of Hg(ClO4)2. Let r identical to [Hg(ClO4)2]added/[DNA-P]. The spectrum of the right-handed form of poly[d(A-T).d(A-T)] turns into that of a seemingly left-handed structure at r greater than or equal to 0.05 while a similar transition is noted with poly[d(G-C).(G-C)] at r greater than or equal to 0.12. The spectral changes are highly cooperative in the long-wavelength region above 250 nm. At r = 1.0, the spectra of the two polymers are more or less mirror images of their CD at r = 0. While most CD bands experience red-shifts upon the addition of Hg(ClO4)2, there are some that are blue-shifted. The CD changes are totally reversible when Hg(II) is removed from the nucleic acids by the addition of a strong complexing agent such as NaCN. This demonstrates that mercury keeps all base pairs in register.     

Equilibrium binding of benzo[a]pyrene tetrol to synthetic polynucleotides: sequence selectivity, thermodynamic properties, and ionic strength dependence

We have investigated the equilibrium binding of racemic 7r,8t,9t,10c-tetrahydroxy-7,8,9,10-tetrahydrobenzo[a]pyrene to the double-stranded, synthetic polynucleotides poly[d(A-T)], poly[d(G-C)], and poly[d(G-m5C)] at low binding ratios. Difference absorption spectroscopy shows a 10-nm red shift for binding to poly[d(A-T)] and an 11-nm red shift for binding to either poly[d(G-C)] or poly[d(G-m5C)]. The value of delta epsilon for binding is approximately the same for all three hydrocarbon-polynucleotide complexes. Binding of this neutral polycyclic aromatic hydrocarbon derivative to these polynucleotides is dependent upon ionic strength and temperature. Analysis of complex formation employing polyelectrolyte theory shows a greater release of counterions associated with binding to poly[d(A-T)] than with the other two polynucleotides (0.5 and ca. 0.36, respectively). Thus, sequence-selective binding of this hydrocarbon in DNA would be expected to change depending on salt concentration. The temperature dependence of binding was studied at 100 mM Na+ where the equilibrium binding constants for poly[d(A-T)] and poly[d(G-m5C)] are roughly equivalent and 6-fold greater than the binding affinity for poly[d(G-C)]. The binding to poly[d(A-T)] and poly[d(G-C)] is characterized by a delta H omicron = -7.0 kcal/mol, and the large difference in affinity constants arises from differences in negative entropic contributions. Formation of hydrocarbon-poly[d(G-m5C)] complexes is accompanied by a delta H = -9.1 kcal/mol. However, the affinity for poly[d-(G-m5C)] is the same as that for poly[d(A-T)] due to the much more negative entropy associated with binding to poly[d(G-m5C)].     

Porphyrin and metalloporphyrin binding to DNA polymers: rate and equilibrium binding studies

Interactions of meso-tetrakis(4-N-methylpyridiniumyl)porphyrin [TMpyP(4)] with poly[d(G-C)].poly[d(G-C)] [poly[d(G-C)2] and poly[d(A-T)].poly[d(A-T)] [poly[d(A-T)2] were studied by equilibrium dialysis and stopped-flow dissociation kinetics as a function of [Na+]. Metalloderivatives of TMpyP(4), NiTMpyP(4), and ZnTMpyP(4) were also investigated. The apparent equilibrium binding constants (Kobs) were approximately the same for TMpyP(4) binding to either poly[d(G-C)2] or poly[d(A-T)2] and decreased with increasing [Na+]. The slopes of the plots of log Kobs vs log [Na+] were similar, with values close to -2.7. Contrary to implications in previously reported studies, these data do not indicate that TMpyP(4) prefers to bind to GC sites at low ionic strength and to AT sites at high ionic strength. In contrast, binding of ZnTMpyP(4) to these two polymers is very different. Comparisons of Kobs values at 0.065 M [Na+] indicate that ZnTMpyP(4) binding to AT sites is approximately 200 times more favorable than binding to GC sites, a finding in agreement with previous qualitative observations. Although the binding of the Zn species to the GC polymer was too weak for us to assess the salt effect, the plot of log Kobs vs log [Na+] gave a slope of -2.0 for ZnTMpyP(4) binding to poly[d(A-T)2]. Application of condensation theory for polyelectrolytes suggests similar charge interactions for ZnTMpyP(4) and for TMpyP(4) binding to poly[d(A-T)2]. Likewise, the rates of dissociation from poly[d(A-T)2] were similar for TMpyP(4) and ZnTMpyP(4) [and also NiTMpyP(4)]. However, whereas TMpyP(4) [and NiTMpyP(4)] dissociation from poly[d(G-C)2] was measurable, that for ZnTMpyP(4) was too fast to measure.(ABSTRACT TRUNCATED AT 250 WORDS)