ISSN:0006-3525    

DOI:10.1002/bip.360230302

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

年代:1984

数据来源: WILEY

摘要:

AbstractEight conformers typical of diketopiperazine (DKP) ring folding were chosen for analysis. Conformational energy calculations were carried out using the semiempirical quantummechanical CNDO/2 method. The results obtained confirm considerable flexibility of the DKP skeleton. As the degree of folding increases, twisted boat conformations with the nonplanar peptide bonds tend to be more stable, while more rigid regular boat conformations with planar peptide bonds appear to be less stable than a flat one. The CNDO/2 method was found to be reliable enough for conformational studies of cyclic peptide skeletons withcis‐peptide bond

ISSN:0006-3525    

DOI:10.1002/bip.360230303

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

年代:1984

数据来源: WILEY

摘要:

AbstractUnwinding of a single cooperatively melting region of ColE1 DNA is investigated by a slow temperature jump in formamide–neutral buffer mixed solvent. The semilogarithmic plots of unwinding relaxation curves show a marked terminal linear region following the fast decay, which occurred within the temperature rise time (1 ∼ 2 s). This longest relaxation is ascribed to the total unwinding of a single cooperatively melting region. The longest relaxation time, τ1, is uniquely determined by the final equilibrium state and becomes shorter as the final temperature increases. Decrease in ionic strength makes τ1and its fractional amplitude increase, and the relaxation almost approaches single‐exponential decay. The facts that (1) τ1of a single cooperatively melting region whose unwinding suffers larger frictional resistance does not always unwind more slowly, as was shown by the observations of τ1's of almost the same cooperatively melting region located at different positions on two linearized ColEl DNAs and of τ1's of two cooperatively melting regions on the same linearized ColEl DNA; (2) τ1has strong dependence on the equilibrium state after a temperature jump; and (3) the observed τ1is much longer than the expected time of the frictional barrier all demonstrate that the τ1is limited by chemical but not hydrodynamic processes. The detailed unwinding process of a single cooperatively melting region, elucidated by evidence of a negative apparent activation energy of the rewinding process and by extensive computer simulation of the equilibrium melting process, suggests that the local heterogeneity of G+C content in a cooperatively melting region, as well as its averaged G+C content, strongly affects its unwinding rate. The present study of a single cooperatively melting region is found to be useful to improve our understanding of the detailed mechanism of complex unwinding of large natural DNAs, in which many cooperatively melting r

ISSN:0006-3525    

DOI:10.1002/bip.360230304

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

年代:1984

数据来源: WILEY

摘要:

AbstractCalculations of the optical properties (absorption, linear dichroism, circular dichroism, and anisotropic components of the CD) are presented for polynucleotides of random or regular sequence within the formalism of the matrix method using a set of parameters that includes only the ππ* transitions of the aromatic bases. Experimental solution spectra agree favorably with calculated CD spectra for A‐RNA, A‐DNA, and B‐DNA, when coordinates derived from x‐ray studies on fibers are used. Excessive hypochromicity is predicted when parameters intended to reproduce the vacuum‐uv absorption of the chromophores are included in the calculations, but total elimination of these parameters leads to an insufficient hypochromicity for the long‐wavelength absorption band. Using alternative conformations for DNA in low‐salt aqueous solution did not improve the agreement between experimental and calculated spectra, but some features of the optical properties predicted for these variant structures suggest that the tilt of the bases with respect to the helical axis may be larger than that of the fiber B‐form.In the case of polynucleotides with regular structure, which have been traditionally less easy to understand in terms of the standard nucleic acid conformations, a series of alternative structures has been examined. Unexpectedly, the calculated spectrum for the Z‐DNA structure compares almost quantitatively with the experimental spectrum of poly(dGC·dGC) in low salt. This result, which confirms a recent report [Vasmel, H.&Greve, J. (1981)Biopolymers20, 1329–1332], is in contrast with the current identification of Z‐DNA with the high‐salt form of poly(dGC·dGC). Finally, the optical properties of single‐stranded polyribonucleotides appear to be better explained when alternative structures [91‐helix for poly(rA) and 61‐helix for poly(rC)] are int

ISSN:0006-3525    

DOI:10.1002/bip.360230305

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

年代:1984

数据来源: WILEY

摘要:

AbstractThe optical modes of DNA that displace one strand against the other are modeled by the motion of an oscillator in an asymmetric quartic double‐well potential whose minima represent the A‐ and B‐conformations. Assuming that the variation of the polarizability during vibration derives mainly from the tilting of the base rings relative to the helix axis, the total polarizability tensor is shown to possess approximately ellipsoidal symmetry and to depend nonlinearly on the instantaneous displacement of the two strands. The Raman spectrum of a collection of randomly oriented molecules is calculated. It consists of one or more peaks with characteristic shape. The depolarization ratio is 3/4, independent of molecular conformation and frequency. The results are discussed in the light of existing experimental and theoretical inform

ISSN:0006-3525    

DOI:10.1002/bip.360230306

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

年代:1984

数据来源: WILEY

摘要:

AbstractComplexes of poly(BU) with various adenine derivatives were investigated by circular dichroism (CD) and absorption spectroscopy. A 1:2 stoichiometry was indicated on CD mixing curves for typical complexes of 9‐substituted adenine and 2‐aminoadenine derivatives with poly(BU). The CD spectrum of adenosine·2poly(BU) is characterized by well‐resolved bands in the range of 210–350 nm. Other adenine derivative–poly(BU) complexes also afford similar CD spectra, while 2‐aminoadenine derivative–poly(BU) complexes give quite different spectra. Attempts to assign representative CD spectra were made using the transition of helical poly(BU) and the respective purine polynucleotides. The similarity of the CD spectra suggests that poly(A)·2poly(BU) and adenine derivative–poly(BU) complexes are nearly identical in structure except for the ribose–phosphate linkage. The fact that the uv isosbestic point of adenosine·2poly(BU) falls in close proximity to that of the corresponding polymer complex also supports this conclusion. In the formation of stable helices, the ribose moiety is dispensable in the “strand” of purine. TheTmof 9‐methyladenine·2poly(BU) is somewhat higher than that of adenosine·2poly(BU) under equivalent conditions. TheTmdifference with the monomer–poly(U) system was found to be about 20°C in 0.4MNaCl–0.02MNa–cacodylate–5 × 10−4MEDTA (pH 7.0). Further, it was noted that the monomer–poly(BU) complexes are formed even when theTm

ISSN:0006-3525    

DOI:10.1002/bip.360230307

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

年代:1984

数据来源: WILEY

摘要:

AbstractUsing the semiempirical potential functions, conformational energies of the model compounds DMP−, d(pCp), d(pGp), and d(pCpGpCp) are calculated, and the B → Z transition is discussed along the pseudorotational path of the sugar ring. For dimethylmonophosphate anion, DMP−, the energy contour map is presented and the stabilities of the phosphodiester conformations discussed. For the sugar ring without the base attached, the minimum energies for each sugar‐puckering form are calculated along the pseudorotational path. The energy barrier of the interconversion between the C(3′)‐endoform and the C(2′)‐endoform is calculated to be about 2.0 kcal/mol. From the conformational energy calculations of the interconversions of mononucleoside diphosphates, d(pCp) and d(pGp), between the C(2′)‐endoconformer and the C(3′)‐endoconformer, the purine sugar segment is known to be more convertible than the pyrimidine sugar segment. The results also support the finding that the pseudorotational transition occurred with the O(1′)‐endoform more easily than with the O(1′)‐exoform. Based on the results of conformational studies of DMP−, d(pCp), and d(pGp), a topological transition of the handedness of the model compound, d(pCpGpCp), is studied. The left‐handed Z‐form is found to be less stable by about 8.5 kcal/mol than is the right‐handed B‐form. The energy barrier of the Z → B transition is calculated to be about 17.4 kcal/mol. The contributions of the electrostatic and nonbonded energies to the energy barrier are discussed in connection with the conformatio

ISSN:0006-3525    

DOI:10.1002/bip.360230308

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

年代:1984

数据来源: WILEY

摘要:

AbstractThe relaxation kinetics of binding of ethidium to calf‐thymus DNA as studied previously by the temperature‐jump method with absorption detection [Bresloff, J.&Crothers, D. M. (1975)J. Mol. Biol.95, 103] is reanalyzed in terms of a series of models for DNA‐ligand interactions that include cases with and without internal and bimolecular direct transfer of ligands between different binding modes or different binding sites. The experimental results are shown to be consistent with two alternative binding mechanisms. Both models include bimolecular “direct transfer” steps and a site size of two base pairs per site. In the first model, there exist two distinct modes of binding to the DNA double helix at each binding site. In the second model, sites containing at least one GC base pair constitute a different and stronger class of binding sites than those containing only AT base pairs. The existence of a direct transfer pathway between two classes of bound ligands is supported by the linear increase of reciprocal relaxation times far beyond the concentration regions, where off‐rates should have become rate limiting. The second model, incorporating the notion of base selectivity, is in quantitative agreement with published work on ethidium binding to DNAs of different base compositions and with nmr measurements of bound ligan

ISSN:0006-3525    

DOI:10.1002/bip.360230309

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

年代:1984

数据来源: WILEY

摘要:

AbstractCation transport through a chloroform liquid membrane by cyclic octapeptides—cyclo(Leu‐Pro)4, cyclo(Phe‐Pro)4, and cyclo[Lys(Z)‐Pro]4—was investigated. All of these cyclic octapeptides transported K+and Ba2+, and the rate of cation transport was correlated with the ability to extract cations from the aqueous phase to the chloroform phase. Among them, cyclo (Leu‐Pro)4was the most efficient and transported K+and Ba2+selectively from other alkali and alkaline earth cations, respectively. The rate of K+transport by cyclo(Leu‐Pro)4was about one‐third as fast as that by dicyclohexyl 18‐crown‐6. Picrate anion transport against its concentration gradient was observed by cyclo(Leu‐Pro)4, which is conjugated with the selective transport of K+. Complex formation in a liposome between cyclo(Leu‐Pro)4and Ba2+was observed, but the b

ISSN:0006-3525    

DOI:10.1002/bip.360230310

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

年代:1984

数据来源: WILEY

摘要:

AbstractThe assignments of31P resonances of eight short oligonucleotides have been achieved through specific heterodecoupling techniques reported previously from our laboratory [Cheng et al. (1982)Biopolymers21, 697–701]. The temperature dependence of theassigned31P chemical shifts of these oligomers was studied and compared to the constitutive dimeric units. This comparison gives some insight to the chemical‐shift values of the phosphorus resonances of oligonucleotides. (1) The 3′‐end terminal phosphorus resonance in an oligomer tends to locate at a spectral position relatively close to its constitutive dimeric unit. (2) On chain elongation (from 5′‐toward 3′‐end), the phosphorus resonance in the oligomer will be shifted upfield by 0.2–0.3 ppm, as compared to its constitutive dimeric unit. (3) The relative positions of phosphorus resonances in an oligomer tend to remain in the same order as their constitutive dimeric units. The above obsrvations lead to the development of a new procedure to assign the31P resonance of a single‐stran

ISSN:0006-3525    

DOI:10.1002/bip.360230311

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

年代:1984

数据来源: WILEY