A Monte Carlo method for generating structures of short single-stranded DNA sequences

A Monte Carlo method has been developed for generating the conformations of short single-stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Minimum energy states of individual dinucleotide monophosphate molecules are identified using a torsion angle minimizer. The glycosyl and acyclic backbone torsions of the dimers are allowed to vary, while the sugar rings are held fixed in one of the two preferred puckered forms. A total of 108 conformationally distinct states per dimer are considered in this first stage of minimization. The torsion angles within 5 kcal/mole of the global minimum in the resulting optimized states are then allowed to vary by ±10° in an effort to estimate the breadth of the different local minima. The energies of a total of 2187 (3⁷) angle combinations are examined per local conformational minimum. Finally, the energies of all dinucleotide conformers are scaled so that the populations of differently puckered sugar rings in the theoretical sample match those found in nmr solution studies. This last step is necessitated by limitations in the theoretical methods to predict DNA sugar puckering accurately. The conformer populations of the individual acyclic torsion angles in the composite dimer ensembles are found to be in good agreement with the distributions of backbone conformations deduced from nmr coupling constants and the frequencies of glycosyl conformations in x-ray crystal structures, suggesting that the low energy states are reasonable. The low energy dimer forms (consisting of 150–325 conformational states per dimer step) are next used as variables in a Monte Carlo algorithm, which generates the conformations of single-stranded d(CX_nG) chains, where X = A, T and n = 3, 4, 5. The oligonucleotides are built sequentially from the 5′ end of the chain using random numbers to select the conformations of overlapping dimer units. The simulations are very fast, involving a total of 10⁶ conformations per chain sequence. The potential errors in the buildup procedure are minimized by taking advantage of known rotational interdependences in the sugar–phosphate backbone. The distributions of oligonucleotide conformations are examined in terms of the magnitudes, positions, and orientations of the end-to-end vectors of the chains. The differences in overall flexibility and extension of the oligomers are discussed in terms of the conformations of the constituent dinucleotide steps, while the general methodology is discussed and compared with other nucleic acid model building techniques. © 1993 John Wiley & Sons, Inc.     

基于高分辨率卫星图的川中丘陵区村级景观格局特征研究

以Erle C.Ellis 建立的村级景观分类和景观制图方法,利用IKONOS高分辨率（1 m）卫星遥感图,进行典型抽样和地形→土地利用→土地覆被→生态立地的景观分类和分层制图,研究了四川盆地中部丘陵地区村级景观的构成和格局特征,并就有关方法作了讨论.结果表明,川中盆地丘陵村级景观类型多样,其多样性指数从地形、土地覆被、土地利用到生态立地变化在1.08～2.26之间,丰富度除土地覆被较高,达到85%以外,其余都较低,在42.22%～58.62%之间.分布普遍的生态立地类型为12.5%,其余88.5%的类型都以较大差异分布在各村级景观内.景观破碎化指数较高,不同村级景观之间为2.93～4.27,地形到生态立地的破碎度为2.86～5.63.村级景观构成中,人口密度、道路面积和农家院落面积与景观格局指数存在较大程度的线性相关关系,但以农家院落面积与景观分形指数、景观破碎度的线性相关显著,分别为0.957*和0.991**.运用景观4级分类和制图方法研究村级景观,多数景观格局指标都表现出显著的统计学差异,表明运用高分辨率卫星遥感图研究村级景观,以多级景观单元分类研究比单一分类的更能够反映相关信息,增加对村级景观格局的认识和理解.     

Frontal cortex and reward-guided learning and decision-making

Reward-guided decision-making and learning depends on distributed neural circuits with many components. Here we focus on recent evidence that suggests four frontal lobe regions make distinct contributions to reward-guided learning and decision-making: the lateral orbitofrontal cortex, the ventromedial prefrontal cortex and adjacent medial orbitofrontal cortex, anterior cingulate cortex, and the anterior lateral prefrontal cortex. We attempt to identify common themes in experiments with human participants and with animal models, which suggest roles that the areas play in learning about reward associations, selecting reward goals, choosing actions to obtain reward, and monitoring the potential value of switching to alternative courses of action.     

A dumbbell-shaped, double-hairpin structure of DNA: a thermodynamic investigation

We report the first calorimetric and spectroscopic investigation on a member of a new class of nucleic acid secondary structures in which both ends of a duplex core are closed by single-stranded loops. Such structures can be formed intramolecularly from appropriately designed base sequences. We have synthesized the 24-mer sequence shown, and we present calorimetric, spectroscopic, and electrophoretic (formula; see text) evidence that it adopts a dumbbell-shaped, double-hairpin structure. Our data allow us to reach the following conclusions: (1) The phosphodiester gap in the center of the core duplex of the dumbbell does not reduce the transition enthalpy relative to that measured for the corresponding octameric duplex d(GGAATTCC)2. (2) Incorporation of a 5'-phosphate group into the gap decreases the thermal stability of the dumbbell relative to its unphosphorylated sequence. On the basis of the salt dependence of this effect, we propose that the phosphorylation--induced decrease in thermal stability is electrostatic in origin. From the changes in the transition enthalpy and entropy, we suggest that the phosphorylation-induced decrease in thermal stability of the double hairpin arises from electrostatically induced based unstacking at the nick. (3) The thymine residues in the loop behave both electrostatically and enthalpically like denatured single strands. Published nuclear magnetic resonance studies reveal partial stacking of thymine residues in the loops of linear hairpin structures. If this feature persists in the double-hairpin structure, then the spatial overlap of thymine residues in the loops does not necessarily produce a favorable enthalpic contribution. (4) When both ends of the nicked octameric core duplex are constrained by loops of only four thymine residues, the dumbbell structure may adopt conformations in which the 5' and 3' ends at the nick are twisted relative to the helical axis and therefore are not in phase. Such conformations would account for the observed resistance of the double-hairpin structure to ligation, since the 3'OH and 5'P would no longer be collinear.     

Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy

Atomic force microscopy (AFM) has been applied in many biological investigations in the past 15 years. This review focuses on the application of AFM for quantitatively characterizing the structural and thermodynamic properties of protein-protein and protein-nucleic acid complexes. AFM can be used to determine the stoichiometries and association constants of multiprotein assemblies and to quantify changes in conformations of proteins and protein-nucleic acid complexes. In addition, AFM in solution permits the observation of the dynamic properties of biomolecular complexes and the measurement of intermolecular forces between biomolecules. Recent advances in cryogenic AFM, AFM on two-dimensional crystals, carbon nanotube probes, solution imaging, high-speed AFM, and manipulation capabilities enhance these applications by improving AFM resolution and the dynamic and operative capabilities of the AFM. These developments make AFM a powerful tool for investigating the biomolecular assemblies and interactions that govern gene regulation.