abstract：:We studied the influence of different 2'-OMe-RNA and DNA strand combinations on single strand targeted foldback triplex formation in the Py.Pu:Py motif using ultraviolet (UV) and circular dichroism (CD) spectroscopy, and molecular modeling. The study of eight combinations of triplexes (D.D:D, R*.D:D, D.D:R*, R*.D:R*, ...

journal_title：Journal of biomolecular structure & dynamics

authors： Kandimalla ER,Venkataraman G,Sasisekharan V,Agrawal S

更新日期：1997-06-01 00:00:00

abstract：:Thermodynamic and structural properties of two UNCG tetraloops in very short hairpin octamers, 5'-r(GCUUCGGC)-3' and 5'-r(GCUACGGC)-3', have been studied by means of various physical techniques. Melting profiles of both octamers, obtained from UV absorption spectra taken as a function of temperature, are consistent wi...

journal_title：Journal of biomolecular structure & dynamics

authors： Abdelkafi M,Ghomi M,Turpin PY,Baumruk V,Hervé du Penhoat C,Lampire O,Bouchemal-Chibani N,Goyer P,Namane A,Gouyette C,Huynh-Dinh T,Bednárová L

更新日期：1997-04-01 00:00:00

abstract：:The results of Raman and Infrared (IR) spectroscopic investigations on the vibrational modes of dimethyl phosphorothioate (DMPS) anion, [(CH3O)2(POS)]-, are reported. Ab initio calculations of the vibrational modes, the IR and Raman spectra and the interatomic force constants of DMPS were performed. A normal mode calc...

journal_title：Journal of biomolecular structure & dynamics

authors： Steinke CA,Reeves KK,Powell JW,Lee SA,Chen YZ,Wyrzykiewicz T,Griffey RH,Mohan V

更新日期：1997-02-01 00:00:00

abstract：:The first fully energy-minimized structures for a series of structurally related metal complexes of the important mammalian metal binding protein metallothionein are described. The structures were calculated based on structural information obtained from existing spectroscopic and crystallographic data, and minimized u...

journal_title：Journal of biomolecular structure & dynamics

authors： Fowle DA,Stillman MJ

更新日期：1997-02-01 00:00:00

abstract：:Alkylamine-substituted naphthalene imides and diimides bind DNA by intercalation and have applications as anticancer agents. The unique structures of these imides in which two adjacent carbonyl groups lie coplanar to an extended aromatic ring system allow the possibility of sequence-selective interactions between the ...

journal_title：Journal of biomolecular structure & dynamics

authors： Liu ZR,Hecker KH,Rill RL

更新日期：1996-12-01 00:00:00

abstract：:A number of tandemly repeated DNA sequences have the ability to form hairpin structures by forming non-standard base pairs. When (GCC)15 and (GGC)15 strands are annealed together, the expected duplex is the only product. However, when (GCC)15 is annealed with (GCC)10, depending on the relative concentrations, up to fi...

journal_title：Journal of biomolecular structure & dynamics

authors： Zhao Y,Cheng W,Gibb CL,Gupta G,Kallenbach NR

更新日期：1996-10-01 00:00:00

abstract：:The design and DNA binding activity of beta-structure-forming peptides and netropsin-peptide conjugates are reported. It is found that a pair of peptides-S,S'-bis(Lys-Gly-Val-Cys-Val-NH-NH-Dns)-bridged by an S-S bond binds at least 10 times more strongly to poly(dG).poly(dC) than to poly(dA).poly(dT). This peptide can...

journal_title：Journal of biomolecular structure & dynamics

authors： Nikolaev VA,Grokhovsky SL,Surovaya AN,Leinsoo TA,Sidorova NYu,Zasedatelev AS,Zhuze AL,Strahan GA,Shafer RH,Gursky GV

更新日期：1996-08-01 00:00:00

abstract：:Repetitive basic polypeptides containing lysine or arginine as every third amino acid were shown to cause DNA condensation at physiological salt concentration connected with selective DNA binding with respect to DNA composition and sequence. This selectivity is very similar to that existing in the case of histone H1 a...

journal_title：Journal of biomolecular structure & dynamics

authors： Sponar J,Votavová H

更新日期：1996-06-01 00:00:00

abstract：:Nuclear quadrupole relaxation is a sensitive measure of electrolyte environments. We used the relaxation of 23Na to probe mobile ion-matrix interactions and the electrostatic structure of the polyelectrolyte extracellular matrix of cartilage. Specifically, we measured spin-lattice and spin-spin relaxation times of 23N...

journal_title：Journal of biomolecular structure & dynamics

authors： Dai H,McFarland EW

更新日期：1996-04-01 00:00:00

abstract：:The recently introduced Essential Dynamics sampling method is extended such that an exhaustive sampling of the available (backbone) configurational space can be achieved. From an initial Molecular Dynamics simulation an approximated definition of the essential subspace is obtained. This subspace is used to direct subs...

journal_title：Journal of biomolecular structure & dynamics

authors： de Groot BL,Amadei A,van Aalten DM,Berendsen HJ

更新日期：1996-04-01 00:00:00

abstract：:An ab initio quantum-chemical study of stacked and hydrogen-bonded protonated cytosine dimer has been carried out. The calculations were made using the second-order Moller-Plesset perturbational method (MP2) with a medium-sized polarized set of atomic orbitals. H-bonded as well as stacked protonated base pairs are mor...

journal_title：Journal of biomolecular structure & dynamics

authors： Sponer J,Leszczynski J,Vetterl V,Hobza P

更新日期：1996-02-01 00:00:00

abstract：:TATA-box binding protein (TBP) in a monomeric form and the complexes it forms with DNA have been elucidated with molecular dynamics simulations. Large TBP domain motions (bend and twist) are detected in the monomer as well as in the DNA complexes; these motions can be important for TBP binding of DNA. TBP interacts wi...

journal_title：Journal of biomolecular structure & dynamics

authors： Miaskiewicz K,Ornstein RL

更新日期：1996-02-01 00:00:00

abstract：:Over the years the structural properties of nucleic acids have been of interest, providing data that may be of importance for DNA and RNA organization and function in the cell. We have attempted to look for the formation of parallel RNA-RNA duplexes in vitro. RNA molecules comprising complementary in the same polarity...

journal_title：Journal of biomolecular structure & dynamics

authors： Tchurikov NA,Ponomarenko NA,Golova YB,Chernov BK

更新日期：1995-12-01 00:00:00

abstract：:DNaseI digestion studies (Brukner et al, EMBO J 14, 1812-1818 1995) and nucleosomebinding data (Satchwell et al, J. Mol. Biol. 191, 639-659 1986, Goodsell and Dickerson, Nucleic trinucleotides. A detailed comparison of the two models suggests that while both of them represent improvements with respect to dinucleotide ...

journal_title：Journal of biomolecular structure & dynamics

authors： Brukner I,Sánchez R,Suck D,Pongor S

更新日期：1995-10-01 00:00:00

abstract：:Under negative superhelical stress, long (TG)n containing repeats experience a stepwise multiple B-Z transitions. We have investigated the effect of the plasmid size on this transitional behavior. A 66-bp (TG)n containing repeat from the 5'-untranscribed region of mouse ribosomal DNA was inserted in a 3-kb, a 6.5-kb a...

journal_title：Journal of biomolecular structure & dynamics

authors： Albert AC,Leng M,Rahmouni AR

更新日期：1995-08-01 00:00:00

abstract：:The structure of the nonclassical pi kappa base pair (7-methyl-oxoformycin B. . .2,4-diaminopyrimidine) was studied at the ab initio Hartree-Fock (HF) and MP2 levels using the 6-31G* and 6-31G** basis sets. The pi kappa base pair is bound by three parallel hydrogen bonds with the donor-acceptor-donor recognition patte...

journal_title：Journal of biomolecular structure & dynamics

authors： Florián J,Leszczyński J

更新日期：1995-04-01 00:00:00

abstract：:A simple statistical approach for the analysis of biological sequences, such as splice-sites, promoter regions, helices and extended structure forming regions or any other sequence dependent functional entities in proteins, is presented. The approach has been proved useful to develop a method for prediction of such en...

journal_title：Journal of biomolecular structure & dynamics

authors： Reddy BV,Pandit MW

更新日期：1995-02-01 00:00:00

abstract：:In the past two decades RNase A has been the focus of diverse investigations in order to understand the nature of substrate binding and to know the mechanism of enzyme action. Although this system is reasonably well characterized from the view point of some of the binding sites, the details of interactions in the seco...

journal_title：Journal of biomolecular structure & dynamics

authors： Seshadri K,Rao VS,Vishveshwara S

更新日期：1994-12-01 00:00:00

abstract：:Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises an important question: are the different conformers in the unit cell artifacts of crystal packing forces, or do they represent different solution state structures? The objective of...

journal_title：Journal of biomolecular structure & dynamics

authors： Arnold GE,Manchester JI,Townsend BD,Ornstein RL

更新日期：1994-10-01 00:00:00

abstract：:Using Fourier transform, we investigate the structural characteristics of genomes for several viruses. The mutual correlations and ordering of the different nucleotides in genomes are compared versus their counterparts from the random sequences with the same nucleotide composition. In order to assess the stastical sig...

journal_title：Journal of biomolecular structure & dynamics

authors： Chechetkin VR,Knizhnikova LA,Turygin AYu

更新日期：1994-10-01 00:00:00

abstract：:Abstract In order to target the major groove of DNA, we have designed novel peptide derivatives of 7-H pyridocarbazole, which is the chromophoric ring of ditercalinium, a potent antitumor bisin- tercalator. We will present here the results obtained with a compound that has a D-Asn tethered to the pyridinium nitrogen...

journal_title：Journal of biomolecular structure & dynamics

authors： Gresh N,René B,Hui XW,Barsi MC,Roques BP,Garbay C

更新日期：1994-08-01 00:00:00

abstract：:It has been shown that the frequency versus size distribution of A and T overlapping and non-overlapping homopolymer tracts of N > 5 in D. discoideum gene flanking and intron regions are significantly greater than in coding regions(1). In the present report, we demonstrate, that a spatial periodicity exists in long A ...

journal_title：Journal of biomolecular structure & dynamics

authors： Marx KA,Hess ST,Blake RD

更新日期：1994-08-01 00:00:00

abstract：:Telomeric DNA sequences are known to adopt unusual DNA structures upon protonation when contained into negatively supercoiled DNA. In this paper, the structural properties of (T2AG3)n telomeric sequences of different length is analyzed in detail. Transition to the protonated form is observed at very low pH for (T2AG3)...

journal_title：Journal of biomolecular structure & dynamics

authors： Huertas D,Lipps H,Azorín F

更新日期：1994-08-01 00:00:00

abstract：:The results of 1-nanosecond molecular dynamics simulations of the enzyme ribonuclease T1 and its 2'GMP complex in water are presented. A classification of the angular reorientations of the backbone amide groups is achieved via a transformation of NH-vector trajectories into several coordinate frames, thus unravelling ...

journal_title：Journal of biomolecular structure & dynamics

authors： Fushman D,Ohlenschläger O,Rüterjans H

更新日期：1994-06-01 00:00:00

abstract：:The structural and energetical characteristics of the complexes formed between two auto-complementary DNA dodecamers, d(CGCGAATTCGCG)2, and d(GCGCAATTGCGC)2, and two novel netropsin (I) and glycine-netropsin (II) conjugates of a tricationic water-soluble porphyrin are investigated in detail by means of theoretical com...

journal_title：Journal of biomolecular structure & dynamics

authors： Perrée-Fauvet M,Gresh N

更新日期：1994-06-01 00:00:00

abstract：:RNA.DNA hybrid duplexes are relevant in various biological mechanisms like transcription and replication. Enzymes like RNase H cleave specifically the RNA strand in RNA.DNA duplexes. In antisense technology the complexation of mRNA with "modified" oligo(deoxy)-nucleotides leads to new hybrid duplexes. The knowledge ab...

journal_title：Journal of biomolecular structure & dynamics

authors： Fritsch V,Wolf RM

更新日期：1994-06-01 00:00:00

abstract：:A simplified multidimensional search was applied to determine the structure of deoxyhexamer CGCGCG in the crystal form belonging to the space group C222(1) (a = 45.6 A, b = 37.3 A, c = 70.3 A). This crystal form contains two Z-DNA duplexes per asymmetric unit in a similar orientation. The search consists of several ma...

journal_title：Journal of biomolecular structure & dynamics

authors： Strokopytov BV,Malinina LV

更新日期：1994-04-01 00:00:00

abstract：:The empirical potential including the intra- and intermolecular energy terms was used to study the interaction of L-Lysine-L-Alanine-L-Alanine Tripeptide with four models of B-DNA with different compositions. On the basis of a detailed search of the respective potential energy surface, it was found that the peptide is...

journal_title：Journal of biomolecular structure & dynamics

authors： Vondrásek J,Sponar J,Hobza P

更新日期：1994-02-01 00:00:00

abstract：:Relative humidity induces the reversible crystal transition of guanosine between the dihydrate and the anhydrous state. The characteristics of the transition was investigated by means of X-ray powder diffraction analysis and high-resolution solid-state 13C NMR spectroscopy. Adsorption-desorption hysteresis was observe...

journal_title：Journal of biomolecular structure & dynamics

authors： Sugawara Y,Iimura Y,Iwasaki H,Urabe H,Saito H

更新日期：1994-02-01 00:00:00

abstract：:With a view to understanding the structural requirement for tyrosine phosphorylation, we have examined the free and Ca(2+)-bound conformations of the synthetic peptide tBoc-Leu-Pro-Tyr-Ala-NHCH3, a substrate for a protein tyrosine kinase, using circular dichroism (CD), 1H and 13C nuclear magnetic resonance (NMR) and m...

journal_title：Journal of biomolecular structure & dynamics

authors： Ananthanarayanan VS,Saint-Jean A,Cheesman BV,Hughes DW,Bain AD

更新日期：1993-12-01 00:00:00

abstract：:Tetra-(4-N-methylpyridyl)-porphyrin, (T4MPyP), is a tetracationic porphyrin that binds to G-C sequences of DNA by means of an intercalative mode. In order to extend its selective sequence recognition capacity for bases beyond the intercalation site, and in the major groove, we have undertaken the theoretical design of...

journal_title：Journal of biomolecular structure & dynamics

authors： Hui X,Gresh N

更新日期：1993-10-01 00:00:00

abstract：:The interaction of calf-thymus DNA with cobalt-hexammine and cobalt-pentammine cations was investigated, in aqueous solution at pH 6-7 with cation/DNA(phosphate) molar ratios r = 1/80, 1/40, 1/20, 1/10, 1/4, 1/2 and 1, using Fourier Transform infrared (FTIR) difference spectroscopy. Correlations between spectral chang...

journal_title：Journal of biomolecular structure & dynamics

authors： Tajmir-Riahi HA,Naoui M,Ahmad R

更新日期：1993-08-01 00:00:00

abstract：:A new algorithm for the analysis of nonselective proton relaxation data in protein solution is presented. T1 and T2 of protein protons in lysozyme and RNase solutions were measured at three resonance frequencies--11, 27 and 90 MHz. In addition we measured water T1 dispersions in lysozyme solutions over the frequency r...

journal_title：Journal of biomolecular structure & dynamics

authors： Krushelnitsky AG,Fedotov VD

更新日期：1993-08-01 00:00:00

abstract：:Stereochemical effects of methylphosphonate (MP) in B-DNA and Z-DNA duplexes are studied through molecular mechanics approach. Duplexes of different lengths, tetramers, hexamers, dodecamers are examined to assess the interstrand and intrastrand electrostatic effects due to MPs vis-a-vis phosphates. A variety of models...

journal_title：Journal of biomolecular structure & dynamics

authors： Swarnalatha Y,Yathindra N

更新日期：1993-06-01 00:00:00

abstract：:NMR experiments with a 21412 Redfield observation pulse were carried out on a kappa-carrageenan aqueous solution containing 0.5M LiI. A detected hydrogen-bonded proton resonance at approximately 17.6 ppm, is in accordance with an ordered carrageenan structure in the solution similar to the double, parallel-stranded he...

journal_title：Journal of biomolecular structure & dynamics

authors： Nerdal W,Haugen F,Knutsen S,Grasdalen H

更新日期：1993-04-01 00:00:00

abstract：:Supercoiling causes global twist of DNA structure and the supercoiled state has wide influence on conformational transition. A statistical mechanical approach was made for prediction of the transition probability to non-B DNA structures under torsional stress. A conditional partition function was defined as the sum ov...

journal_title：Journal of biomolecular structure & dynamics

authors： Katsura S,Makishima F,Nishimura H

更新日期：1993-02-01 00:00:00

abstract：:Virtually all mRNA sequences carry a 3-base periodical pattern, presumably involved in the translation frame monitoring mechanism (Trifonov, E.N., J. Mol. Biol. 194, 643-652, 87). The hidden pattern, 5'-(GHN)n-3' (H representing nonG, N any base), is further refined by extensive computational analysis of mRNA sequence...

journal_title：Journal of biomolecular structure & dynamics

authors： Lagunez-Otero J,Trifonov EN

更新日期：1992-12-01 00:00:00

abstract：:We have applied random-search, energy minimization and molecular dynamics simulations to investigate the structural aspects of the interaction of N-acetyl-L-prolyl-D-alanyl-L-alanine-N'-methylamide with Ca2+. Spectral data on related peptides had suggested that the beta-turn conformation might be a prerequisite for th...

journal_title：Journal of biomolecular structure & dynamics

authors： Michel AG,Jeandenans C,Ananthanarayanan VS

更新日期：1992-10-01 00:00:00

abstract：:The conformational changes of poly(d2NH2A-dT) in aqueous solution, induced by increasing the NaCl concentration from 0.1M to 4M, have been monitored by ultraviolet resonance Raman spectroscopy, in using the 222-, 257- and 281 nm excitation wavelengths. These changes have been interpreted in comparing the polymer spect...

journal_title：Journal of biomolecular structure & dynamics

authors： Mojzes P,Chinsky L,Turpin PY,Miskovsky P

更新日期：1992-08-01 00:00:00

abstract：:Regulation of gene expression in eukaryotes involves a complex assembly of DNA recognition sequence elements and their respective protein factors. The upstream promoter/enhancer sequences are position and orientation independent. Despite their variable distances from the TATA box and transcription start site, interact...

journal_title：Journal of biomolecular structure & dynamics

authors： Nussinov R

更新日期：1992-06-01 00:00:00