摘要:

AbstractThe general formulas describing the low‐angular dependence of polarized (Vv) and depolarized (Hv) light‐scattering intensity by a chain macromolecule of arbitrary form with anisotropic polarizability are derived. It is shown that the valuedHv/dtHvo(wheret= [〈R2〉S/L]2,Sbeing the scattering vector) is an indication of the chain‐flexibility mechanism. This permits one to distinguish between the models of a wormlike chain, regular zigzag, or statistical zigzag. The results of numerical calculations useful for the interpretation of experimental data are

ISSN:0006-3525    

DOI:10.1002/bip.1978.360170102

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

年代:1978

数据来源: WILEY

摘要:

AbstractThe kinetics of the fluorescence decay of the energy donor in a homologous series of oligopeptides each containing at its ends a donor and an acceptor of electronic excitation energy was investigated in solvent mixtures of different viscosities. The repeating unit in the peptides wasN5‐(2‐hydroxyethyl)‐L‐glutamine and the chromophores used as donor and acceptor were naphthalene and dansyl, respectively. The number of units in the peptides studied varied from four to nine. The solvents used were mixtures of glycerol and trifluoroethanol in various proportions. The decay rate of the donor fluorescence increases when the solvent viscosity decreases. This behavior is due to the disturbance of the equilibrium end‐to‐end distribution of distance of the excited molecules by the energy transfer process, which is more favorable foe short than for long distances. The subsequent rearrangement towards the equilibrium distribution by diffusion of the molecular ends relative to one another enhances the efficiency of the energy transfer. Assuming a modified Fick equation to describe this diffusion motion, the fluorescence decay data were analyzed in terms of a diffusion coefficient describing the Brownian motion of the molecular ends. The diffusion coefficients thus evaluated increase systematically upon decreasing the solvent viscosity. For example, for the oligopeptides studied it changes from unmeasurably small values in glycerol solution to values varying between 10−8to 10−7cm2/sec at room temperature in a glycerol trifluoroethanol solvent mixture of viscosity of 8 centipoise. The values obtained for the diffusion coefficient are smaller by about an order of magnitude than the values expected for the diffusion coefficients of the free chromophores in solvents of comparable viscosity. It is thus concluded that the backbone of the polymeric chains possesses appreciable internal friction which exerts resistance to the Brownian motion of the polymer chains. The diffusion coefficient of the end‐to‐end motion is systematically smaller for the shorter than for the longer chains. For example, at room temperature in a solvent mixture of 8 centipoise it is 3×10−8, 5×10−8, 7.6×10−8, and 8.5×10−8cm2/sec for oligomers containing four, five, eight, and nineN5‐(2‐hydroxylethyl)‐L‐glutamine repeating units, respectively. The internal friction thus impedes the motion of the molecular ends more effectively in the shorter chains than in the longer ones.Analysis of the energy‐transfer experiments in solvents spanning a wide range of viscosities shows that the orientational factor appearing in Förster's equation for energy transfer does not interfere perceptibly with the evaluation of the end‐to‐end distances from the fluorescence decay data when naphthalene and dansyl serve as donor and acceptor, respectively. This is due to the fact that both the donor emission and acceptor absorption in the range of spectral overlap are characterized by more than one transition dipole moment, as is ev

ISSN:0006-3525    

DOI:10.1002/bip.1978.360170103

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

年代:1978

数据来源: WILEY

摘要:

AbstractThe sugar–phosphate–sugar complex C10H18O8P, a unit of the polynucleotide chains, was analyzed, making use of 100 conformational energies computed in the Hartree‐Fock approximation with a small basis set of Gaussian type orbitals. The geometry of the conformations [which corresponds to the C(2′)‐endodeoxy system], the basis set, and the computed total energies are reported in this work. In addition, a number of attempts are presented where we searched for a computationally very simple analytical expression apt to fit, with reasonable accuracy, the computed energies. Lennard‐Jones type potential seems to offer an appropriate form capable of reproducing the positions of the maxima and the minima resulting fromab initiocomputations, but neither the 6‐12 nor other similar forms seem to be able to correctly reproduce the intensity of the barriers. Form a details analysis of the barriers to rotation about the bonds O(5′)—C(5′) and C(5′)—C(4′) in terms of nonboned interactions, we found that a substantial improvement in the fit of analytical toab initioenergies may be obtained by distinguishing between atoms characterized by the same atomic number but having different chemical characteristics, like the oxygen atoms of the phosphate group, on one hand, and the oxygen atoms of the sugar rings and the hydr

ISSN:0006-3525    

DOI:10.1002/bip.1978.360170104

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

年代:1978

数据来源: WILEY

摘要:

AbstractIn the first paper of this series we showed that the total electronic energy, computedab initioin the Hartree‐Fock approximation for both independent and coupled rotations of the five torsional angles in the sugar–phosphate–sugar complex C10H18O8P, can be reproduced with reasonable accuracy by a Lennard‐Jones 6‐12 potential, with different attractive and repulsive parameters assigned to the four oxygens of the phosphate group, on one hand, and the four oxygens of the sugar rings and the hydroxyl groups, on the other. The conclusion was reached on the basis of some attempts at the derivation of analytical expressions capable of correctly describing the energies obtained with the quantum mechanical computations. An analysis of the barriers to internal rotation for the angles φ and ψ indicated the possibility of improving the description through addition of further terms, in particular of an intrinsic torsional potential. In order to obtain a fit based on all internal rotations of the sugar–phosphate–sugar molecules, and coupling numerical accuracy with physical significance, we made a study of the possible contributions to the conformational energy: intrinsic torsional energy, electrostatic interactions, London attractions, van der Waals repulsions. The results of this study show that the best description ofab initioenergies is offered by a potential containing a Lennard‐Jones 6‐12 term and an intri

ISSN:0006-3525    

DOI:10.1002/bip.1978.360170105

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

年代:1978

数据来源: WILEY

摘要:

AbstractConformational energy maps for the four combinations of two consecutive torsional angles of the backbone structure of polydeoxyribonucleotides are presented. Both the C(2′)‐endoand the C(3′)‐endoconformation of sugar rings were considered. The energies were evaluated with an analytical expression representing the best fit toab initioenergies computed in the Hartree‐Fock approximation, and consisting of a contribution from nonbonded interactions of the Lennard‐Jones 6‐12 type and an intrinsic torsional potential. It is shown that the minima of these maps are in excellent agreement with the most stable conformations as obtained from x‐ray crystallographic analysis of nucleic acids and

ISSN:0006-3525    

DOI:10.1002/bip.1978.360170106

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

年代:1978

数据来源: WILEY

摘要:

AbstractWe have tested 21 different basis sets of synthetic DNA circular dichroism spectra and have slected one for use in spectral analyses of natural DNAs. This “standard” set consists of spectra of eight polymers: poly[d(A‐A‐T)·d(A‐T‐T)], poly[d(A‐G‐G)·d(C‐C‐T)], poly[d(A‐T)·d(A‐T)], poly[d(G‐C)·d(G‐C)], poly[d(A‐G)·d(C‐T)], poly[d(A‐C)·d(G‐T)], poly[d(A‐T‐C)·d(G‐A‐T)], and poly[d(A‐G‐C)·d(G‐C‐T)]. This basis set, applied according to the first‐neighbor polymer procedure of Gray and Tinoco, allows a more uniformly accurate spectral analysis of six natural complex DNAs and eight (A+T)‐rich satellite DNAs for base composition and first‐neighbor frequencies than was previously possible. We find that spectra of poly[d(A)·d(T)] and/or poly[d(A‐C‐T‐)·d(A‐G‐T)]are not generally required for good analysis results but we show in this and the following paper that t

ISSN:0006-3525    

DOI:10.1002/bip.1978.360170107

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

年代:1978

数据来源: WILEY

摘要:

AbstractFrom an analysis of their circular dichroism spectra, we find that the four (A + T)‐rich satellite DNAs ofDrosophila nasutoideshave distributions of first‐neighbor base paris that resemble those previously found for other (A + T)‐richDrosophilasatellites. We also apply our spectral analysis procedure for the first time to two (G + C)‐rich satellite DNAs, those from the hermit crabPagurus pollicaris. We find thatP. pollicarissatellite I cannot be accurately analyzed with our standard set of spectral components and thatP. pollicarissatellite II appears to be much like the synthetic polymer poly[d(A‐G‐C‐)·d(G‐C‐T)] in its firs

ISSN:0006-3525    

DOI:10.1002/bip.1978.360170108

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

年代:1978

数据来源: WILEY

摘要:

Abstract13C spin‐lattice relaxation times (T1's) of four cyclic hexapeptides of sequence, (X‐L‐Pro‐Y)2, are reported. TheT1's of the protonated carbons, which undergo dipolar relaxation, are interpreted qualitatively in terms of the overall tumbling motion of the molecule and in terms of internal motion. It is found that three of the cyclic hexapeptides, those which adopt all‐transβ‐conformers, tumble isotropically and appear to lack internal motion in the peptide backbone. The method of Torchia and Lyerla was applied to these compounds in order to compare the mobility of the proline rings. The results show that the sequence and particular type of β‐turn present affect the internal motion of the Pro ring. Data on a fourth cyclic hexapeptide, which occurs in a conformation with two‐cis X‐Pro bonds, suggests that internal motion of the backbone contributes an additional frequency component to the motion of theYresidue α‐carbons. A consideration of the mobility of the proline rings in the conformer with two‐cispeptide bonds revealed that they are significantly more rigid in the two‐cisstruc

ISSN:0006-3525    

DOI:10.1002/bip.1978.360170109

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

年代:1978

数据来源: WILEY

摘要:

AbstractRaman spectroscopic studies have been carried out on polymers ofL‐valine ranging in degree of polymerization (DP) from 2 to 930. The spectrum of the hexapeptide (DP= 6) is closely similar over the entire range 40–1750 cm−1to those of polymers with much higherDP, and the structure is clearly shown to be that of the antiparallel pleated sheet (β‐structure) by the amide I and III frequencies. The formation of a little α‐helical structure occurs in polymers withDPabove 500, although the amount does not appear to be a linear function ofDP. The α‐helical structure is unstable and readily destroyed in samples cast from trifluoroacetic acid solution. It is stabilized by the incorporation ofL‐alanine, a strong helix‐former; polymers of the latter may in turn be forced into a α‐structure in copolymers suffici

ISSN:0006-3525    

DOI:10.1002/bip.1978.360170110

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

年代:1978

数据来源: WILEY

摘要:

AbstractWe have measured the ultraviolet CD spectra for covalently closed and linear forms of phage PM2 DNA in solution. We find that increased concentrations of salt or ethanol (up to 50% ethanol by weight) depress the long‐wavelength positive CD bands in the spectra of both forms of DNA, although the spectrum of the native covalently closed DNA always has a slightly larger magnitude of these bands than does the spectrum of the linear DNA. In addition, both DNAs are equally capable of undergoing a transition to the A conformation in 70–80% ethanol at low Na+concentrations. Thus, the constraint imposed by the covalent closure of a DNA molecule does not seem to hinder its conformational response to these changing solution conditions. Lang [(1973)J. Mol. Biol.78, 247–254] has found by electron microscopy that T7 DNA has an inherent ability to condense into compact particles, suggested to be supercoils of multiple order. Both covalently closed and linear forms of PM2 DNA also become condensed when the DNA, in 0.2Mammonium acetate and 1 mMEDTA, is exposed to ethanol and subsequent drying on specimen grids [Lang, D., Taylor, T. N., Dobyan, D. C.&Gray, D. M. (1976)J. Mol. Biol.106, 97–107]. Under similar conditions, in solutions of 0.2Mammonium acetate and 1 mMEDTA to which ethanol is added, we have measured the CD spectra of both covalently closed and linear forms of DNA. Below ethanol concentrations at which the DNA obviously precipitates, the CD spectra of both forms have reduced long‐wavelength positive

ISSN:0006-3525    

DOI:10.1002/bip.1978.360170111

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

年代:1978

数据来源: WILEY