Minor-groove width and accessibility in B-DNA drug and protein complexes.

A new definition is presented for minor-groove width in double-helical B-DNA structures. This uses interstrand H4' ... H5' rather than P ... P distances. It is shown by examination of various oligonucleotide crystal structures that these H4' ... H5' distances are a sensitive measure of minor-groove drug and protein binding, since these hydrogen atoms are in direct non-bonded contact with such bound ligands.     

Groove Width and Depth of B-DNA Structures Depend on Local Variation in Slide

Abstract

The groove widths of DNA helix, especially minor groove width, are generally believed to be important for recognition of DNA by various types of ligands. It has been postulated earlier that large negative propeller twist, in the AT rich regions compresses the minor groove of duplex DNA A systematic study has now been carried out by generating models with different values of local doublet and intra-basepair parameters and calculating their minor groove widths. It is found that several local doublet parameters affect the minor groove width but it depends most strongly on the local step parameters roll and slide when each parameter is considered individually. However, a detailed analysis of the various local parameters within the B-DNA family of crystal structures indicates that propeller twist and slide are most strongly correlated with the observed values of minor groove width. The groove depth is also strongly correlated with slide. Thus the local base sequence dependent variations in slide can modify both the groove width and depth and consequently determine the ligand binding properties of DNA.     

Mg(2+) in the Major Groove Modulates B-DNA Structure and Dynamics

This study investigates the effect of Mg(2+) bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5'-CpA or TpG. Based on this knowledge, molecular dynamics simulations were carried out on a DNA oligomer without or with Mg(2+) close to an ApG step. These simulations showed that the hydrated Mg(2+) forms a stable intra-strand cross-link between the two purines in solution. ApG generates an electrostatic potential in the major groove that is particularly attractive for cations; its intrinsic conformation is well-adapted to the formation of water-mediated hydrogen bonds with Mg(2+). The binding of Mg(2+) modulates the behavior of the 5'-neighboring step by increasing the BII (ε-ζ>0°) population of its phosphate group. Additional electrostatic interactions between the 5'-phosphate group and Mg(2+) strengthen both the DNA-cation binding and the BII character of the 5'-step. Cation binding in the major groove may therefore locally influence the DNA conformational landscape, suggesting a possible avenue for better understanding how strong DNA distortions can be stabilized in protein-DNA complexes.     

Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps.

The structurally correlated dihedral angles epsilon and zeta are known for their large variability within the B-DNA backbone. We have used molecular modelling to study both energetic and mechanical features of these variations which can produce BI/BII transitions. Calculations were carried out on DNA oligomers containing either YpR or RpY dinucleotides steps within various sequence environments. The results indicate that CpA and CpG steps favour the BI/BII transition more than TpA or any RpY step. The stacking energy and its intra- and inter-strand components explain these effects. Analysis of neighbouring base pairs reveals that BI/BII transitions of CpG and CpA are easiest within (Y)n(R)n sequences. These can also induce a large vibrational amplitude for TpA steps within the BI conformation.     

Analysis of local helix geometry in three B-DNA decamers and eight dodecamers

Local variations in B-DNA helix structure are compared among three decamers and eight dodecamers, which contain examples of all ten base-pair step types. All pairwise combinations of helix parameters are compared by linear regression analysis, in a search for internal relationships as well as correlations with base sequence. The primary conclusions are: (1) Three-center hydrogen bonds between base-pairs occur frequently in the major groove at C-C, C-A, A-A and A-C steps, but are less convincing at C-C and C-T steps in the minor groove. The requirements for large base-pair propeller are (1) that the base-pair should be A.T rather than G.C, and (2) that it be involved in a major groove three-center hydrogen bond with the following base-pair. Either condition alone is insufficient. Hence, a large propeller is expected at the leading base-pair of A-A and A-C steps, but not at A-T, T-A, C-A or C-C steps. (2) A systematic and quantitative linkage exists between helix variables twist, rise, cup and roll, of such strength that the rise between base-pairs can hardly be described as an independent variable at all. Two typical patterns of behavior are observed at steps from one base-pair to the next: high twist profile (HTP), characterized by high twist, low rise, positive cup and negative roll, and low twist profile (LTP), marked by low twist, high rise; negative cup and positive roll. Examples of HTP are steps G-C, G-A and Y-C-A-R, where Y is pyrimidine and R is purine. Examples of LTP steps are C-G, G-G, A-G and C-A steps other than Y-C-A-R. (3) The minor groove is especially narrow across the two base-pairs of the following steps: A-T, T-A, A-A and G-A. (4) In general, base step geometry cannot be correlated solely with the bases that define the step in question; the two flanking steps also must be taken into account. Hence, local helix structure must be studied in the context, not of two base-pairs: A-B, but of four: x-A-B-y. Calladine's rules, although too simple in detail, were correct in defining the length of sequence over which a given perturbation is expressed. Whereas ten different two-base steps are possible, allowing for the identity of complementary sequences, there are 136 different four-base steps. Only 33 of these 136 four-base steps are represented in the decamer and dodecamer structures solved to date, and hence it is premature to try to set up detailed structural algorithms. (5) The sugar-phosphate backbone chains of B-DNA place strong limits on sequence-induced structural variation, damping down most variables within four or five base-pairs, and preventing purine-purine anti-anti mismatches from causing bulges in the double helix. Hence, although short-range sequence-induced deformations (or deformability) are observed, long-range deformations propagated down the helix are not to be expected.     

Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing.

Crystal structures of B-form DNA have provided insights into the global and local conformational properties of the double helix, the solvent environment, drug binding and DNA packing. For example, structures of the duplex with sequence CGCGAATTCGCG, the Dickerson-Drew dodecamer (DDD), established a unique geometry of the central A-tract and a hydration spine in the minor groove. However, our knowledge of the various interaction modes between metal ions and DNA is very limited and almost no information exists concerning the origins of the different effects on DNA conformation and packing exerted by individual metal ions.Crystallization of the DDD duplex in the presence of Mg(2+)and Ca(2+)yields different crystal forms. The structures of the new Ca(2+)-form and isomorphous structures of oligonucleotides with sequences GGCGAATTCGCG and GCGAATTCGCG were determined at a maximum resolution of 1.3 A. These and the 1.1 A structure of the DDD Mg(2+)-form have revealed the most detailed picture yet of the ionic environment of B-DNA. In the Mg(2+)and Ca(2+)-forms, duplexes in the crystal lattice are surrounded by 13 magnesium and 11 calcium ions, respectively.Mg(2+)and Ca(2+)generate different DNA crystal lattices and stabilize different end-to-end overlaps and lateral contacts between duplexes, thus using different strategies for reducing the effective repeat length of the helix to ten base-pairs. Mg(2+)crystals allow the two outermost base-pairs at either end to interact laterally via minor groove H-bonds, turning the 12-mer into an effective 10-mer. Ca(2+)crystals, in contrast, unpair the outermost base-pair at each end, converting the helix into a 10-mer that can stack along its axis. This reduction of a 12-mer into a functional 10-mer is followed no matter what the detailed nature of the 5'-end of the chain: C-G-C-G-A-ellipsis, G-G-C-G-A-ellipsis, or a truncated G-C-G-A-ellipsis Rather than merely mediating close contacts between phosphate groups, ions are at the origin of many well-known features of the DDD duplex structure. A Mg(2+)coordinates in the major groove, contributing to kinking of the duplex at one end. While Ca(2+)resides in the minor groove, coordinating to bases via its hydration shell, two magnesium ions are located at the periphery of the minor groove, bridging phosphate groups from opposite strands and contracting the groove at one border of the A-tract.     

Ring width and vessel features of the mangrove Excoecaria agallocha L. depend on salinity in the Sundarbans,Bangladesh

The Bangladesh Sundarbans is the largest continuous mangrove in the world that providing crucial environmental services, particularly related to coastal protection and livelihoods of millions of people. However, anthropogenic disturbances, diseases infestation and environmental changes including sea level rise (SLR) and fresh-water flux into the delta are threatening the Sundarbans and other mangrove ecosystems worldwide. Protection of mangrove ecosystems requires knowledge on factors that mainly drive growth and vitality of tree species to evaluate which consequences can be expected from, mainly hydrology-related, environmental changes. In this study, we assessed the nature and periodicity of tree rings in Excoecaria agallocha, a wide spread mangrove species in the Bangladesh Sundarbans. We also analysed the influence of climatic factors, such as precipitation, temperature and vapor pressure deficit (VPD), and river discharge, as a proxy of salinity on ring width (RW) and vessel features, such as mean vessel area (MVA) and mean vessel density (MVD). E. agallocha forms distinct tree-ring boundary that characterized by a narrow (2–4 cells wide) band of radially flattened fibres. The RW as well as the MVA and MVD are crossdatable. The RW is mainly driven by salinity which is influenced by freshwater inputs through precipitation during monsoon along with river discharge January to April. The MVA and MVD responded to similar seasons and months as RW, but mostly with opposite signs in MVD. The results suggest that fresh water inputs through precipitation and river discharge positively influence the radial growth of E. agallocha in the Sundarbans. The RW and vessel features can be used as proxies to explore the growth dynamics of this species, especially in relation to global environmental changes.     

Bending and curvature calculations in B-DNA.

A simple program, BEND, has been written to calculate the magnitude of local bending and macroscopic curvature at each point along an arbitrary B-DNA sequence, using any desired bending model that specifies values of twist, roll and tilt as a function of sequence. The program has been used to evaluate six different DNA bending models in three categories. Two are bent non-A-tract models: (a) A new model based on the nucleosome positioning data of Satchwell et al 1986 (J. Mol. Biol. 191, 659-675), (b) The model of Calladine et al 1988 (J. Mol. Biol. 201, 127-137). Three are bent A-tract models: (c) The wedge model of Bolshoy et al 1991 (Proc. Natl. Acad. Sci. USA 88, 2312-2316), (d) The model of Cacchione et al 1989 (Biochem. 28, 8706-8713), (e) A reversed version of model (b). The last is a junction model: (f) The model of Koo & Crothers 1988 (Proc. Natl. Acad. Sci. USA 85, 1763-1767). Although they have widely different assumptions and values for twist, roll and tilt, all six models correctly predict experimental A-tract curvature as measured by gel retardation and cyclization kinetics, but only the new nucleosome positioning model is successful in predicting curvature in regions containing phased GGGCCC sequences. This model--showing local bending at mixed sequence DNA, strong bends at the sequence GGC, and straight, rigid A-tracts--is the only model consistent with both solution data from gel retardation and cyclization kinetics and structural data from x-ray crystallography.     

Social effects on foraging behavior and success depend on local environmental conditions

In social groups, individuals' dominance rank, social bonds, and kinship with other group members have been shown to influence their foraging behavior. However, there is growing evidence that the particular effects of these social traits may also depend on local environmental conditions. We investigated this by comparing the foraging behavior of wild chacma baboons, Papio ursinus, under natural conditions and in a field experiment where food was spatially clumped. Data were collected from 55 animals across two troops over a 5‐month period, including over 900 agonistic foraging interactions and over 600 food patch visits in each condition. In both conditions, low‐ranked individuals received more agonism, but this only translated into reduced foraging performances for low‐ranked individuals in the high‐competition experimental conditions. Our results suggest one possible reason for this pattern may be low‐ranked individuals strategically investing social effort to negotiate foraging tolerance, but the rank‐offsetting effect of this investment being overwhelmed in the higher‐competition experimental environment. Our results also suggest that individuals may use imbalances in their social bonds to negotiate tolerance from others under a wider range of environmental conditions, but utilize the overall strength of their social bonds in more extreme environments where feeding competition is more intense. These findings highlight that behavioral tactics such as the strategic investment of social effort may allow foragers to mitigate the costs of low rank, but that the effectiveness of these tactics is likely to be limited in certain environments.     

Effects of experimental warming on biodiversity depend on ecosystem type and local species composition

Climatic warming is a primary driver of change in ecosystems worldwide. Here, we synthesize responses of species richness and evenness from 187 experimental warming studies in a quantitative meta‐analysis. We asked 1) whether effects of warming on diversity were detectable and consistent across terrestrial, freshwater and marine ecosystems, 2) if effects on diversity correlated with intensity, duration, and experimental unit size of temperature change manipulations, and 3) whether these experimental effects on diversity interacted with ecosystem types. Using multilevel mixed linear models and model averaging, we also tested the relative importance of variables that described uncontrolled environmental variation and attributes of experimental units. Overall, experimental warming reduced richness across ecosystems (mean log‐response ratio = –0.091, 95% bootstrapped CI: –0.13, –0.05) representing an 8.9% decline relative to ambient temperature treatments. Richness did not change in response to warming in freshwater systems, but was more strongly negative in terrestrial (–11.8%) and marine (–10.5%) experiments. In contrast, warming impacts on evenness were neutral overall and in aquatic systems, but weakly negative on land (7.6%). Intensity and duration of experimental warming did not explain variation in diversity responses, but negative effects on richness were stronger in smaller experimental units, particularly in marine systems. Model‐averaged parameter estimation confirmed these main effects while accounting for variation in latitude, ambient temperature at the sites of manipulations, venue (field versus lab), community trophic type, and whether experiments were open or closed to colonization. These analyses synthesize extensive experimental evidence showing declines in local richness with increased temperature, particularly in terrestrial and marine communities. However, the more variable effects of warming on evenness were better explained by the random effect of site identity, suggesting that effects on species’ relative abundances were contingent on local species composition. Synthesis A global research priority is to understand the consequences of climate change for biodiversity. A growing number of experimental studies have manipulated climatic drivers, in particular changes in temperature, in local communities. In the first quantitative meta‐analysis of community‐level studies across freshwater, marine and terrestrial experiments, species richness declined consistently with experimental warming. This effect was insensitive to warming intensity, duration, and multiple environmental and procedural covariates. However, evenness responses were weakly negative only in terrestrial systems and more variable across ecosystem types. Linear mixed model analyses revealed that the identity of local sites explained nearly 50% of variance in evenness effect sizes, compared to only 10% for richness. This result provides evidence that local species composition strongly constrains changes in relative species abundances in response to warming.     

Base sequence, local helix structure, and macroscopic curvature of A-DNA and B-DNA

Given a specified DNA sequence and starting with an idealized conformation for the double helix (A-DNA or B-DNA), the dependence of conformational energy on variations in the local geometry of the double helix can be examined by computer modeling. By averaging over all thermally accessible states, it is possible to determine 1) how the optimum local structure differs from the initial idealized conformation and 2) the energetic costs of small structural deformations. This paper describes such a study. Tables are presented for the prediction of helix twist angles and base pair roll angles for both A-DNA and B-DNA when the sequence has been specified. Local deviations of helix parameters from their average values can accumulate to produce a net curvature of the molecule, a curvature that can be sharp enough to be experimentally detectable. As an independent check on the method, the calculations provide predictions for the longitudinal compressibility (Young's modulus) and the average torsional stiffness, both of which are in good agreement with experimental values. In examining the role of sequence-dependent variations in helix structure for the recognition of specific sequences by proteins, we have calculated the energy needed to deform the self-complementary hexanucleotide d(CAATTG) to match the local geometry of d(GAATTC), which is the sequence recognized by the EcoRI restriction endonuclease. That energy would be sufficient to reduce the binding of the incorrect sequence to the protein by over 2 orders of magnitude relative to the correct sequence.     

Nucleic acid-metal interactions: V. The effect of silver(I) on the structures of A- and B-DNA forms

The interaction of silver(I) with DNA has been studied with uv LD in aqueous solution and in a humid anisotropic poly(vinyl alcohol) host (B-DNA) and also in 80% ethanolic solution (A-DNA). Addition of silver ions has a pronounced effect on the dichroic spectra of DNA, indicating that the DNA structure is significantly altered. By correlation with calculated reduced LD spectra, using intensities and moments of the corresponding electronic transitions of the DNA bases, the experimental spectra of DNA at high silver content may be interpreted in terms of tilt and roll angles of the bases in the double helix. In ethanolic A-DNA solution there is a pronounced decrease in the orientation by flow of DNA, suggesting that the complexation of DNA to silver may be accompanied by the formation of compact tertiary structures.     

Structural and thermodynamic studies on the adenine.guanine mismatch in B-DNA.

The structure of the synthetic dodecamer d(CGCAAATTGGCG) has been shown by single crystal X-ray diffraction methods to be that of a B-DNA helix containing two A(anti).G(syn) base pairs. The refinement, based on data to a resolution of 2.25 A shows that the mismatch base pairs are held together by two hydrogen bonds. The syn-conformation of the guanine base of the mismatch is stabilised by hydrogen bonding to a network of solvent molecules in both the major and minor grooves. A pH-dependent ultraviolet melting study indicates that the duplex is stabilised by protonation, suggesting that the bases of the A.G mispair are present in their most common tautomeric forms and that the N(1)-atom of adenine is protonated. The structure refinement shows that there is some disorder in the sugar-phosphate backbone.     

Visualization of planar drug intercalations in B-DNA.

A computerized linked-atom modeling system was developed to examine the stereochemical requirements for intercalation of planar drugs into DNA. All classes of conformational possibilities for extending the polynucleotide backbone were examined for their ability to accommodate insertion of a drug into a base-paired region of DNA compatible with adjacent regions of B-DNA while stacking interactions, steric strain and non-bonded interatomic contacts were optimised. One conformation was found which proved superior to all others in ability to satisfy these criteria: an extension of the backbone by characteristic changes in two torsion angles to trans values, plus a change in one sugar puckering to C3'-endo to relieve strain in an adjacent residue. The turn angle distributed over three polynucleotides for this most general mode of intercalation is 90 degrees, equivalent to a helical unwinding of -18 degrees for B-DNA.     

Multiple DNA secondary structures in perfect inverted repeat inserts in plasmids. Right-handed B-DNA, cruciforms, and left-handed Z-DNA

The capabilities of five recombinant plasmids, containing relatively long (approximately 60-100 base pairs) perfect inverted repeat (IR) inserts, to support supercoil stabilized non-B-DNA structures were studied in vitro. The IRs were also alternating purine-pyrimidine sequences, thus, each could form either left-handed Z-DNA or cruciforms. Single-strand specific endonucleases, restriction endonucleases and methylases, and OsO4 modifications were used to characterize the DNA structures. Two-dimensional gel electrophoretic studies indicated that three of the five IRs formed both cruciforms and Z-DNA. (C-G) containing inserts preferred to form Z-DNA, whereas (T-G) sequences favored cruciforms. In vivo supercoil relaxation experiments demonstrated the existence of cruciforms in Escherichia coli. The physiological significance of these structures is discussed.     

塔克拉玛干沙漠腹地柽柳年轮宽度对地下水埋深的响应

【目的】柽柳作为干旱荒漠生态系统的典型物种,研究其年轮宽度对地下水响应的保护有重要价值。【方法】研究基于沙漠腹地达理雅博依绿洲地下水埋深资料,利用年轮测定方法分析不同地下水埋深状况下柽柳年轮宽度的变化,探讨其与地下水埋深变化的关系。【结果】样地一地下水埋深随时间逐年增加,埋深范围是1.2～2.6 m,柽柳的年轮宽度在2001-2020年呈显著增加趋势,变化范围为0.98～5.80 mm,年轮宽度年际间差异显著;样地二地下水埋深随时间增长呈现先增加后减小的趋势,埋深范围是2.7～4.5 m,柽柳年轮宽度在1977-2020年整体呈正弦函数变化,范围为1.46～4.41 mm,年轮宽度年际间差异性不显著;样地一柽柳标准年表振幅范围是0.502～1.641,大于样地二柽柳标准年表振幅范围为0.577～1.331。【结论】样地一地下水埋深向着柽柳生长适宜的范围增加时,有利于柽柳的生长,表现为年轮宽度增加,样地二的柽柳年轮宽度变化和地下水埋深之间无显著相关性。