摘要:

AbstractA new series of x‐ray fiber diffraction patterns is reported from agarose films dried at temperatures close to 100°C from water or dimethylacetamide solutions, cooled to room temperature, stretched above 40°C, and finally x‐rayed at room temperature. This procedure gives x‐ray patterns showing highly crystalline forms of agarose with projected axial advances (h) per repeating disaccharide in the range of 0.888–0.973 nm, and favoring extended and single agarose chains. Stretching the films below 40°C yields an oriented but fairly diffuse x‐ray pattern, similar to that reported previously for agarose, and that has been interpreted in terms of a model with two semicontracted agarose chains, with a value ofh= 0.634 nm, draping around each other to form a double helix.The new data requires that double‐helix to single‐chain transitions be considered in condensed films as well as in solution. Alternatively, two populations of double‐helix and single‐helix conformations may coexist in the same film, or the original case for the double‐helix model may be flawed, perhaps through misinterpretation of the diffuse x‐ray pattern. The new results have prompted a critical discussion of evidence for the double‐helix model and to indicate that there is potential to improve the data experimentally with a view to gaining a clearer insight into the molecular mechanisms invol

ISSN:0006-3525    

DOI:10.1002/bip.360280802

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

年代:1989

数据来源: WILEY

摘要:

AbstractA possible mechanism for regulating the lateral growth of collagen fibrils in vivo is considered. A growth inhibitor associated with a particular part of the long semiflexible collagen molecule restricts that part of the molecule to the surface of the growing assembly. Lateral accretion ceases when these inhibitors form a complete circumferential layer around the fibril surface. Cell‐mediated removal of the inhibitors allows lateral growth to proceed to a second limiting layer, and so on to subsequent limiting layers. In this way, cycles of inhibitor removal and limited lateral accretion permit growth to be synchronized over large populations of fibrils. Observed diameter distributions in bundles of embryonic and neonatal fibrils are those expected from a mechanism of this kind. The mechanism depends on the existence of axial order (D‐periodicity) in fibrils, but not on any specific lateral packing of molecules. Rather, contacts between newly assembled molecules are presumed to be partly fluid‐like in lateral directions (except where covalent cross‐links have formed). Some initial fluidity in lateral packing prior to cross‐linking does not preclude the subsequent emergence of quasi‐crystalline packing as cross‐links form. The cylindrical shape of fibrils in vivo may also be attributable in part to fluidity of intermolecular contacts at the gr

ISSN:0006-3525    

DOI:10.1002/bip.360280803

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe linear dichroism is calculated for DNA fragments in their thermal bending equilibrium. These calculations are given for relatively short fragments, where bent molecules can be described by an arc model. Using the measured value of 350 Å for the persistence length, the limit dichroism (corresponding to complete alignment) decreases due to thermal bending, e.g., for a fragment with 100 base pairs to 80% of the value expected for straight molecules. Thermal bending should lead to a strong continuous decrease of the dichroism with increasing chain length, which is not observed, however, in electric dichroism experiments due to electric stretching. The influence of the electric field on the bending equilibrium is described by a contribution to the bending energy, which is calculated from the movement of charge equivalents against the potential gradient upon bending. The charge equivalents, which are assigned to the helix ends, are derived from the dipole moments causing the stationary degree of orientation. By this procedure the energy term inducing DNA stretching is given for induced, permanent, and saturating induced dipole models without introduction of any additional parameter. The stationary dichroism at a given electric field strength is then calculated according to an arc model by integration over all angles of orientation of helix axes or chords with respect to the field vector, and at each of these angles the contribution to the dichroism is calculated by integration over all helices with different degrees of bending. Orientation functions obtained by this procedure are fitted to dichroism data measured for various restriction fragments. Optimal fits are found for an induced dipole model with saturation of the polarizability. The difference between orientation functions with and without electric stretching is used to evaluate dichroism bending amplitudes. Both chain length and field strength dependence of bending amplitudes are consistent with experimental amplitudes derived from the dichroism decay in low salt buffers containing multivalent ions like Mg2+, spermine, or [(CoNH3)6]3+. Bending amplitudes can be used to evaluate the persistence length from electrooptical data obtained for a single DNA restriction fragment. Bending and stretching effects are considerable already at relatively low chain length, and thus should not be neglected in any quantitative evaluation of experimental data

ISSN:0006-3525    

DOI:10.1002/bip.360280804

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

年代:1989

数据来源: WILEY

摘要:

AbstractEffect of glycine and NaCl on the thermal denaturation of β‐lactoglobulin was examined. The results showed that the transition temperature of β‐lactoglobulin is increased by the addition of glycine and NaCl at 0.5 and 1M. This observed stabilization by glycine and NaCl was interpreted in terms of their favorable interactions with the native state of β‐lactoglobulin and unfavorable interactions with the denatur

ISSN:0006-3525    

DOI:10.1002/bip.360280805

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

年代:1989

数据来源: WILEY

摘要:

AbstractA calorimetric study at 25°C is reported on the interaction between allosteric bovine seminal ribonuclease and cytidine‐3′‐phosphate. The results are compared with those obtained under identical experimental conditions for the interaction of pancreatic ribonuclease A and the same nucleotide. The analysis of the data provides evidence that the binding sites of seminal ribonuclease for cytidine‐3′‐phosphate are not equivalent, in agreement with previous equilibrium dialysis studies. A model with two sites with different affinities toward the nucleotide, the site with higher affinity resembling the binding site of pancreatic ribonuclease, is proposed. The values calculated for the thermodynamic parameters provide an insight of the forces involved in the interaction of the two enzymes with th

ISSN:0006-3525    

DOI:10.1002/bip.360280806

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe electrophoretic mobility of restriction fragments of lambda DNA in agarose gels declines if the field is intermittent rather than continuous, with a greater effect on the longer fragments. The changes are compatible with the assumption of two exponential relaxation processes for field‐dependent configurational changes, one when the field is turned on and another when it terminates. The length dependence at the extrapolated limit of mobility for short pulses with long intervals corresponds closely to the simple inverse proportionality to length expected from theoretical considerations when the molecular configuration is not affected by the electric field. Simple intermittent fields would allow separation of longer molecules than can ordinarily be resolved. The relaxation times for both the change in conformation imposed by the field and the return to field‐free conformation vary as approximately the second power of the length of the molecule, independent of the salt concentration or field strength and varying only slightly with gel density. These relations are not in good agreement with properties expected from reptation theory, and they suggest that a different mechanism must be invoked for the electrophoretic migration of long DNA molecules at ordinary values of field stren

ISSN:0006-3525    

DOI:10.1002/bip.360280807

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

年代:1989

数据来源: WILEY

摘要:

AbstractWe have calculated the expected absorption of microwave radiation in the gigaHertz frequency range by fixed‐length DNA polymer molecules dissolved in saline solution. While the effects of counterions and solvent dynamics have been accounted for in detail, the features of the absorption are completely dominated by the interaction between the charged polymer and the so‐called first hydration layer, that is, the nearest layer of solvent water molecules not actually bonded to the polymer. The relevant parameters of the interaction are the strength of the water‐to‐polymer coupling and the average persistence time of the individual water‐to‐polymer bonds. These are presumably hydrogen bonds to the oxygen atoms of the backbone phosphate structure. Using a given parameterization we can obtain the structured absorption corresponding to compressional wave phonon excitations on the polymer, “organ pipe” modes, such as have been claimed to be seen by Edwards, Davis, Swicord, and Saffer. While further studies have not confirmed these resonances, at some frequency and hydration these modes must become visible because of the high relaxation time measured by Lindsay, the existence of the resonances in relatively dry fibers and films of DNA, and the existence of underdamped modes in the ir spectrum of DNA in solution.We have examined the effects of varying slat concentration and the system temperature. In both cases the effects are virtually nil, in the former because of the Manning condensation phenomenon that preserves a remarkably constant polymer environment over a wide range of bulk ionic strength, and in the latter case because of a fortuitous competition between effects of bulk viscosity and persistence time changes with temperature. Hence any effects seen in the experimental variation of temperature or salinity could be wholly attributed to their modification of the hydration l

ISSN:0006-3525    

DOI:10.1002/bip.360280808

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe intrinsic pK values, as well as the free fractions of sodium and calcium counterions, were determined on salt‐free solutions of amidated pectinates and amidated pectates. The apparent pK values were non dependent of the degree of amidation but only to the effective charge density of the pectic polymers and an unique value of 2.9 ± 0.1 was found for the intrinsic pK value. The results obtained by conductimetry and with (sodium and calcium) specific electrodes showed a blockwise distribution of amide and acid groups in amidated pectates and a blockwise distribution of amide groups and a rather statistical distribution of acid groups in amidated pectinat

ISSN:0006-3525    

DOI:10.1002/bip.360280809

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

年代:1989

数据来源: WILEY

摘要:

AbstractWe have previously described [K. M. Sullivan and D. M. J. Lilley (1986)Cell47, 817–827] a set of sequences, called C‐type inducing sequences, which cause cruciform extrusion by adjacent inverted repeats to occur by an abnormal kinetic pathway involving a large denatured region of DNA. In this paper we apply statistical thermodynamic DNA helix melting theory to these sequences. We find a marked correlation between the ability of sequences to confer C‐type cruciform character experimentally and their calculated propensity to undergo cooperative melting, and no exceptions have been found. The correlations are both qualitative and quantitative. Thus the ColE1 flanking sequences behave as single melting units, while the DNA of the S‐type plasmid pIRbke8 exhibits no propensity to melt in the region of the bke cruciform. The results of the calculations are also fully consistent with the following experimental observations:1the ability of the isolated colL and colR fragments of the ColE1 flanking sequences, as well as the short sequence col30, to confer C‐type character;2C‐type induction by an A + T richDrosophilasequence;3low‐temperature cruciform extrusion by an (AT)34sequence;4the effect of changing sequences at a site 90 base pairs (bp) removed from the inverted repeat;5the effects of systematic deletion of the colL sequence; and6the effects of insertion of various sequences in between the colL sequence and the xke inverted repeat.These studies show that telestability effects on thermal denaturation as predicted from equilibrium helix melting theory of linear DNA molecules may explain all the features that are revealed by studying the extrusion of cruciforms in circular DNA molecules subjected to superh

ISSN:0006-3525    

DOI:10.1002/bip.360280810

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

年代:1989

数据来源: WILEY

摘要:

AbstractBy use of agarose gel electrophoresis, the sieving of spherical particles in agarose gels has been quantitated and modeled for spheres with a radius (R) between 13.3 and 149 mm. For quantitation, the electrophoretic mobility has been determined as a function of agarose percentage (A). Because a previously used model of sieving [D. Rodbard and A. Chrambach (1970)Proc. Natl. Acad. Sci. USA65, 970–977] was found incompatible with some of these data, alternative models have been tested. By use of an underivatized agarose, two models, both based on the assumption of a single effective pore radius (PE) for eachA, were found to yieldPEvalues that were independent ofRand that were in agreement with values ofPEobtained independently (PE= 118 nm ×A−0.74): sieving by altered hydrodynamics in a cylindrical tube of radius,PE, and sieving by steric exclusion from a circular hole of radius,PE. The same analysis applied to a 6.5% hydroxyethylated commercial agarose yileded a steeperPEvsAplot and also agreement of the above tow models with the data. ThePEvsAplot was significantly altered by both further hydroxyethylation and factors that cause variation in the electro‐osmosis found in commercial a

ISSN:0006-3525    

DOI:10.1002/bip.360280811

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

年代:1989

数据来源: WILEY