摘要:

AbstractA theory of polyelectrolyte effects on site‐binding equilibria is generalized to multivalent ligands, multivalent supporting salt, intercalation, and multiple‐site exclusion. The theory, which contains no adjustable parameters, except the number of sites excluded by a bound ligand, gives the dependence of the equilibrium constant on the binding fraction and the salt concentration. The theory is compared with prior experimental data for the dissociation of poly(acrylic acid), the binding of magnesium to polyphosphate, and the binding of ethidium and actionomycin D to DNA. The theory predicts the binding fraction dependence of the dissociation constant of poly(acrylic acid) well. The theory predicts the binding fraction dependence of the association constant of the binding of Mg2+to polyphosphate well, if either one or two phosphates are bound by a magnesium ion. We conclude that polyelectrolyte effects on drug‐DNA equilibria must be substantial. It follows that an incorrect estimate of the number of sites excluded by a bound drug molecule (because of its size or some other nonpolyelectrolyte effect) can be obtained from binding data if polyelectrolyte effects are ignored. The estimate is also within the context of, and subject to the validity of, the model used to describe the nonpolyelectrolyte contribution to binding. Our results suggest that, subject to these conditions, the anticooperativity of the binding of ethidium to DNA might be explained solely in terms of polyelectrolyte effects, and without reference to multiple‐site exclusion, if sequence‐specificity effects can be safely ignored. Our results also suggest that as few as two base pairs might be excluded by an actinomycin molecule. The theory gives fairly good agreement for the salt‐concentration dependence of the association constant of all of the systems studied, including the complex of the neutral drug actinomyc

ISSN:0006-3525    

DOI:10.1002/bip.360231202

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractThe magnetic circular dichroism (MCD) of adenine, hypoxanthine, and guanosine 5′‐diphosphate reveals that, for each species, the uv‐absorption band near 200 nm is composed of at least two electronic transitions. The theory of MCD shows that the dipoles of these transitions are not parallel to one another. The transitions are assigned within the framework of current theories of the electronic structure of the purines. Knowledge of the presence of more than one transition within an absorption envelope is important in interpreting the corresponding natural CD of DNA an

ISSN:0006-3525    

DOI:10.1002/bip.360231203

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractThe electrophoretic mobilities of double‐stranded (ds) DNAs and ds RNAs of various lenths,L, were measured in gels of 0.4–1.8% (w/v) agarose at a voltage gradient of 1.0 V/cm. Differences in the electrophoresis of ds DNA and ds RNA are presented and discussed. A general expression is derived that describes the electrophoretic mobility,M, of either type of ds nucleic acid as a function of the gel concentration and the nucleic acid length:M=M′1(L/L0)−x−M2, whereM′1andL0are constants, andxandM2depend on the agarose gel concentration. The results obtained by fitting our data with this equation are consistent with the mobilities of nucleic acids in a wide range of gel concentrations, including free electrophoresis in solution and electrophoresis in gles of high agarose concentration in which nuleic acids are expected to reptate through the gel matrix. Finally, various methods of plotting agarose gel electrophoresis data ar

ISSN:0006-3525    

DOI:10.1002/bip.360231204

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractThe static accessibility discrete charge algorithm for protein charge interactions is extended to the case of linear polyelectrolytes. In this model, the effective dielectric value between surface charge sites depends predominantly on the solvent ionic strength and the solvent accessibilities of the charge sites. This treatment accounts for the phenomena of specific ion binding in the context of a general electrostatic effect [Matthew and Richards (1982)Biochemistry21, 4989]. Specific ion sites are determined by locating areas of high electrostatic potential at the solvent interface of the macromolecule. At a given ionic strength the calculated potential at a site is taken to describe a binding constant and therefore the ion site occupancy. For a 20‐base‐pair fragment of B‐DNA, net charge of −40, 16 ion sites are indicated in the minor groove. The partial occupancy of each site increases from 0.2 to 0.5 as the ionic strength is increased from 0.01 to 0.50. Over the same range of ionic strength, the electrostatic free energy of this charge array is calculated to change from +0.6 to −0.05 kcal/bp. Parallel behavior is predicted for A‐ and Z‐DNA charge geometries. The most stable configuration, based on electrostatic criteria, at high ionic strength (I= 0.1–0.5) is that of Z‐DNA. In this range, the ratio of “bound” sodium to phosphate is predicte

ISSN:0006-3525    

DOI:10.1002/bip.360231205

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractThe addition of polyethylene glycol (PEG) of MW 6000 to solutions of oxy‐ and deoxyhemoglobins results in an increase in the thermodynamic activity of these proteins. This in turn results, when PEG concentration is high enough, in phase separation into two phases; a protein‐rich, PEG‐poor phase and a PEG‐rich, protein‐poor phase. With increasing PEG concentration, the protein‐rich amorphous phase becomes metastable and is converted into a well‐defined crystalline or polymer phase. The logarithm of protein solubility is a linear function of PEG content up to a protein concentration of 150 g/L because the expression for the activity coefficient can, up to this concentration range, be approximated by a logarithmic function. Curvature appears at higher protein concentrations. Activities obtained by extrapolation from linear portions of the function, showing an unchanged, well‐defined crystalline state, yield an activity coefficient for the saturated PEG‐free protein solution in agreement with the appropriate values obtained from hard‐sphere calculations of excluded volume [Ross, P. D.&Minton, A. P. (1977)J. Mol. Biol.112, 437–452]. Solutions containing two hemoglobin species showed cocrystallization of the hemoglobins with a triple point where two crystal forms ca

ISSN:0006-3525    

DOI:10.1002/bip.360231206

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractConformational energy computations were carried out on the packing of two identical collagenlike poly(tripeptide) triple helices in order to determine the energetics of favorable packing arrangements as a function of composition and chain length. The triple helices considered were [CH3CO‐(Gly‐Pro‐Pro)nt‐NHCH3]3and [CH3CO‐(Gly‐Pro‐Ala)nt‐NHCH3]3, withnt= 3, 4, and 5. The packing arrangements were characterized in terms of their intermolecular energies and orientation angles Ω0of the axes of the two triple helices. For short triple helices (nt= 3 or 4), many low‐energy orientations, with a wide range of values of Ω0, can occur. When the triple helices are longer (nt= 5), the only low‐energy packing arrangements of two poly(Gly‐Pro‐Pro) triple helices are those with a nearly parallel orientation of the two helix axes, with Ω0≈ −10°. This result accounts for the observed parallel (rather than antiparallel) arrangement of collagen molecules in microfibril assembly and stands in contrast to the preferred antiparallel arrangement of a pair of α‐helices. Since the preference for a parallel arrangement of these collagenlike triple helices is less pronounced in the case of poly(Gly‐Pro‐Ala), it appears that this preference is a consequence of the frequent presence of imino acids in position Y of the Gly‐X‐Y repeating triplet. In poly(Gly‐Pro‐Ala), most of the low‐energy packing arrangements are parallel, but a few arrangements with low energies and high values of |Ω0| occur. These packing arrangements have a high energy, however, when Pro is substituted for Ala, and thus they are not accessible for collagen with natural amino (imino) acid sequences. The computations reported here account for some of the characteristic features of collagen packing in terms of the local

ISSN:0006-3525    

DOI:10.1002/bip.360231207

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractA solution to the three‐dimensional Poisson‐Boltzmann equation, generalized to include the finite size of the ions, is presented for the environment of DNA in the B‐ and Z‐conformations. The results clearly indicate that despite the lower linear charge density of the left‐handed Z‐conformer, there is a higher concentration of Na+at the immediate surface of the Z‐from than at the surface of the B‐form. The average concentration of counterions within a 12‐Å radius of the DNA is, nonetheless, higher for the B‐ than for the Z‐form. Calculations of the electrostatic interactions of these conformers with an environment of 0.01Mmonovalent salt show that the salt exerts a greater stabilizing effect on the left‐handed conformer than

ISSN:0006-3525    

DOI:10.1002/bip.360231208

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractThe interactions between inorganic cations and κ‐carrageenan in aqueous solutions have been studied using microcalorimetry. The enthalpy of dilution and the enthalpy of mixing of κ‐carrageenan in the coil conformation with an alkaline metal chloride have been investigated and are in agreement with theoretical predictions. The formation of helical dimer in a K+salt form in the absence of a gel formation is conf

ISSN:0006-3525    

DOI:10.1002/bip.360231209

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractAt low salt ([Na+] = 10−3M), spermidine is capable of transforming DNA from a highly extended random coil to a compact particle. The transition takes place at a spermidine concentration of around 25 μMand the compact particle has been previously studied in considerable detail for several different DNAs. The objective of the present study is to see what effect, if any, spermidine has on T7 DNA conformationpriorto collapse using flow dichroism and intrinsic viscosity. We conclude that increasing the spermidine concentration from 0 to the collapse transition point (above 20 μM) makes DNA increasingly nondraining. Furthermore, the persistence length dropped from 785 (±42) to 560 (±32) to 445 (±26) Å on increasing the ambient spermidine concentration from 0 to 1 to 10 μM. These results are in good agreement with counterion condensation theory and Odijk's theory of the electrostatic contribution to the persistence length of DNA. Nonetheless, it is concluded that counterion condensation is not entirely responsible for DNA collapse and that crosslinking promotes the transition to the compa

ISSN:0006-3525    

DOI:10.1002/bip.360231210

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY

摘要:

AbstractA generalized procedure to generate nucleic acid structures is presented. In this procedure, the bases of a base pair are oriented first for characterization of particular DNA receptor sites. The resultant sites are then used in the study of specific molecule–DNA interactions. For example, intercalation sites, kinked DNA, and twisted and tilted bases are envisioned. Alterations of structures viaanti→synorientations of bases, as well as crankshaft motion about collinear bonds, provide additional conformations without disrupting the overall backbone structure. These approaches to the generation of nucleic acid structures are envisioned as required in studies of the intercalation phenomenon, minor adjustments of DNA to accommodate denaturation, binding of carcinogens to DNA, complex formation of transition metals with DNA, and antitumor agents as ligands. For these base‐pair and base orientations, backbone orientations are calculated by the AGNAS technique to yield physically meaningful conformations, namely, those conformations for which nonbonded contacts are favourable. A procedure is presented to generate dimer duplex units that are physically meaningful and to assemble these units into a polynucleotide duplex. Double helices that begin with B‐DNA, undergo a transition to one of the above‐mentioned receptor sites, and return to B‐DNA can be assembled from a catalog of dimer duplexes. Stereographic projections of the various receptor sites already being used to model binding to DNA ar

ISSN:0006-3525    

DOI:10.1002/bip.360231211

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1984

数据来源: WILEY