Simple molecular engineering of glycol nucleic acid: Progression from self-pairing to cross-pairing with cDNA and RNA

The acyclic chiral nucleic acid analogue, Glycol Nucleic Acid (GNA), displayed exceptional structural simplicity and atom economy while forming self-paired duplexes, using canonical Watson–Crick base pairing. We disclose here that the replacement of phosphodiester linker in GNA with somewhat rigid and shorter carbamate linker in Glycol Carbamate Nucleic Acid (GCNA) backbone allows unprecedented stability to the antiparallel self-paired duplexes. The R-GCNA oligomers were further found to form cross-paired antiparallel duplexes with cDNA and RNA following Watson–Crick base pairing. The stability of cross-paired GCNA:DNA and GCNA:RNA duplexes was higher than the corresponding DNA:DNA and DNA:RNA duplexes. The chiral (R) and (S) precursors were easily accessible from naturally occurring l-serine.     

Homologous Chromosome Pairing in Drosophila melanogaster Proceeds through Multiple Independent Initiations

The dynamics by which homologous chromosomes pair is currently unknown. Here, we use fluorescence in situ hybridization in combination with three-dimensional optical microscopy to show that homologous pairing of the somatic chromosome arm 2L in Drosophila occurs by independent initiation of pairing at discrete loci rather than by a processive zippering of sites along the length of chromosome. By evaluating the pairing frequencies of 11 loci on chromosome arm 2L over several timepoints during Drosophila embryonic development, we show that all 11 loci are paired very early in Drosophila development, within 13 h after egg deposition. To elucidate whether such pairing occurs by directed or undirected motion, we analyzed the pairing kinetics of histone loci during nuclear cycle 14. By measuring changes of nuclear length and correlating these changes with progression of time during cycle 14, we were able to express the pairing frequency and distance between homologous loci as a function of time. Comparing the experimentally determined dynamics of pairing to simulations based on previously proposed models of pairing motion, we show that the observed pairing kinetics are most consistent with a constrained random walk model and not consistent with a directed motion model. Thus, we conclude that simple random contacts through diffusion could suffice to allow pairing of homologous sites.     

Red blood cell rouleaux formation in dextran solution: dependence on polymer conformation

The velocity of rouleaux formation (RF), as previously shown, increases with increasing dextran concentration up to a critical concentration (C_a), beyond which the addition of dextran reduces the RF velocity (RFV). de Gennes' model for polymer solutions suggests that dextrans exist in two conformations: a coil structure at low concentrations, which changes to a network beyond a critical concentration (C^*). In the present study we examined the relation between C_a and C^* for dextrans of different molecular weight, and found that they coincide. This suggests that the change in dextran behavior, from increasing to decreasing RFV, occurs when their conformation changes from coil to network. In addition, it has been reported that in dilute dextran solutions the intercellular distance (D) between RBC in rouleaux increases with the molecular weight of the dextran. We found that D correlates with R_f, the end-to-end distance of the polymer molecule, and for all dextrans D ≤ 1.5 R_f. In accord with de Gennes' Model for polymers between surfaces, this corresponds to intercellular interaction with two overlapping surface-associated polymer layers, which may extend “tails” to interact with the opposing cells. Received: 8 August 1997 / Accepted: 28 November 1997     

Protein-Mediated Chromosome Pairing of Repetitive Arrays

Chromosomally integrated arrays of lacO and tetO operator sites visualized by LacI and TetR repressor proteins fused with GFP (green fluorescent protein) (or other fluorescent proteins) are widely used to monitor the behavior of chromosomal loci in various systems. However, insertion of such arrays and expression of the corresponding proteins is known to perturb genomic architecture. In several cases, juxtaposition of such arrays located on different chromosomes has been inferred to reflect pairing of the corresponding loci. Here, we report that a version of TetR-GFP mutated to disrupt GFP dimerization (TetR-A206KGFP or “TetR-kGFP”) abolishes pairing of tetO arrays in vivo and brings spatial proximity of chromosomal loci marked with those arrays back to the wild-type level. These data argue that pairing of arrays is caused by GFP dimerization and thus presents an example of protein-assisted interaction in chromosomes. Arrays marked with another protein, TetR-tdTomato, which has a propensity to form intramolecular dimers instead of intermolecular dimers, also display reduced level of pairing, supporting this idea. TetR-kGFP provides an improved system for studying chromosomal loci with a low pairing background.     

Minimal folding pathways for coarse-grained biopolymer fragments

The minimal folding pathway or trajectory for a biopolymer can be defined as the transformation that minimizes the total distance traveled between a folded and an unfolded structure. This involves generalizing the usual Euclidean distance from points to one-dimensional objects such as a polymer. We apply this distance here to find minimal folding pathways for several candidate protein fragments, including the helix, the β-hairpin, and a nonplanar structure where chain noncrossing is important. Comparing the distances traveled with root mean-squared distance and mean root-squared distance, we show that chain noncrossing can have large effects on the kinetic proximity of apparently similar conformations. Structures that are aligned to the β-hairpin by minimizing mean root-squared distance, a quantity that closely approximates the true distance for long chains, show globally different orientation than structures aligned by minimizing root mean-squared distance.     

Spatial confinement is a major determinant of the folding landscape of human chromosomes

The global architecture of the cell nucleus and the spatial organization of chromatin play important roles in gene expression and nuclear function. Single-cell imaging and chromosome conformation capture-based techniques provide a wealth of information on the spatial organization of chromosomes. However, a mechanistic model that can account for all observed scaling behaviors governing long-range chromatin interactions is missing. Here we describe a model called constrained self-avoiding chromatin (C-SAC) for studying spatial structures of chromosomes, as the available space is a key determinant of chromosome folding. We studied large ensembles of model chromatin chains with appropriate fiber diameter, persistence length and excluded volume under spatial confinement. We show that the equilibrium ensemble of randomly folded chromosomes in the confined nuclear volume gives rise to the experimentally observed higher-order architecture of human chromosomes, including average scaling properties of mean-square spatial distance, end-to-end distance, contact probability and their chromosome-to-chromosome variabilities. Our results indicate that the overall structure of a human chromosome is dictated by the spatial confinement of the nuclear space, which may undergo significant tissue- and developmental stage-specific size changes.     

Threshold, wave and cell-cell avalanche behaviour in a class of substrate inhibition oscillators.

Two molecules of IgG need to be in close proximity upon a cell surface in order to bind complement. Here we obtain approximate results for the probability that two or more IgG molecules are closer than some minimum separation distance, given that N IgG molecules are bound to the cell. Determining this probability exactly is a classical unsolved problem in geometrical probability. We also estimate the probability of having n pairs of IgG molecules in close proximity and compute the expected number of IgG pairs. Our theoretical results are compared with experimental measurements on complement fixation by IgG.     

Forced-unfolding and force-quench refolding of RNA hairpins

Nanomanipulation of individual RNA molecules, using laser optical tweezers, has made it possible to infer the major features of their energy landscape. Time-dependent mechanical unfolding trajectories, measured at a constant stretching force (f_S) of simple RNA structures (hairpins and three-helix junctions) sandwiched between RNA/DNA hybrid handles show that they unfold in a reversible all-or-none manner. To provide a molecular interpretation of the experiments we use a general coarse-grained off-lattice Gō-like model, in which each nucleotide is represented using three interaction sites. Using the coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of f_S and the loading rate (r_f). The simulations and theoretical analysis have been done both with and without the handles that are explicitly modeled by semiflexible polymer chains. The mechanisms and timescales for denaturation by temperature jump and mechanical unfolding are vastly different. The directed perturbation of the native state by f_S results in a sequential unfolding of the hairpin starting from their ends, whereas thermal denaturation occurs stochastically. From the dependence of the unfolding rates on r_f and f_S we show that the position of the unfolding transition state is not a constant but moves dramatically as either r_f or f_S is changed. The transition-state movements are interpreted by adopting the Hammond postulate for forced-unfolding. Forced-unfolding simulations of RNA, with handles attached to the two ends, show that the value of the unfolding force increases (especially at high pulling speeds) as the length of the handles increases. The pathways for refolding of RNA from stretched initial conformation, upon quenching f_S to the quench force f_Q, are highly heterogeneous. The refolding times, upon force-quench, are at least an order-of-magnitude greater than those obtained by temperature-quench. The long f_Q-dependent refolding times starting from fully stretched states are analyzed using a model that accounts for the microscopic steps in the rate-limiting step, which involves the trans to gauche transitions of the dihedral angles in the GAAA tetraloop. The simulations with explicit molecular model for the handles show that the dynamics of force-quench refolding is strongly dependent on the interplay of their contour length and persistence length and the RNA persistence length. Using the generality of our results, we also make a number of precise experimentally testable predictions.     

Hfq proximity and orientation controls RNA annealing

Regulation of bacterial gene networks by small non-coding RNAs (sRNAs) requires base pairing with messenger RNA (mRNA) targets, which is facilitated by Hfq protein. Hfq is recruited to sRNAs and mRNAs through U-rich- and A-rich-binding sites, respectively, but their distance from the sRNA–mRNA complementary region varies widely among different genes. To determine whether distance and binding orientation affect Hfq’s chaperone function, we engineered ‘toy’ RNAs containing strong Hfq-binding sites at defined distances from the complementary target site. We show that RNA annealing is fastest when the distal face of Hfq binds an A-rich sequence immediately 3′ of the target. This recruitment advantage is lost when Hfq binds >20 nt away from the target, but is partially restored by secondary structure that shortens this distance. Although recruitment through Hfq’s distal face accelerates RNA annealing, tight binding of six Us to Hfq’s proximal face inhibits annealing. Finally, we show that ectopic A-rich motifs dramatically accelerate base pairing between DsrA sRNA and a minimal rpoS mRNA in the presence of Hfq, demonstrating that proximity and orientation predict the activity of Hfq on long RNAs.     

Chromosome synapsis in hexaploids

Theoretical relationships between pachytene multivalent and bivalent frequencies in hexaploids are deduced from a model, based on chromosomes showing sequential association at equidistant pairing sites and uniform propensities for partner exchange throughout their lengths. These relationships approach a limit as the number of pairing sites tends to infinity and the intervals between them tend to zero; at the limit pairing is continuous and the quadrivalent/sexivalent ratio is at a minimum. A maximum of 34·3% of the complement is expected to form quadrivalents when there are two pairing sites per chromosome but this peak is reduced by increasing numbers of pairing sites to a limit of 29·6% when pairing is continuous. Where chromosome length is proportional to the number of pairing sites there will be a log/linear relationship between bivalent frequency and chromosome length otherwise a log/log relationship is expected. In the light of these conclusions, observations on experimental hexaploids could be used to provide estimates of the number of pairing sites on each chromosome.     

DNA Motion Capture Reveals the Mechanical Properties of DNA at the Mesoscale

Single-molecule studies probing the end-to-end extension of long DNAs have established that the mechanical properties of DNA are well described by a wormlike chain force law, a polymer model where persistence length is the only adjustable parameter. We present a DNA motion-capture technique in which DNA molecules are labeled with fluorescent quantum dots at specific sites along the DNA contour and their positions are imaged. Tracking these positions in time allows us to characterize how segments within a long DNA are extended by flow and how fluctuations within the molecule are correlated. Utilizing a linear response theory of small fluctuations, we extract elastic forces for the different, ∼2-μm-long segments along the DNA backbone. We find that the average force-extension behavior of the segments can be well described by a wormlike chain force law with an anomalously small persistence length.     

Elastic thickness compressibilty of the red cell membrane

We have used an ultrasensitive force probe and optical interferometry to examine the thickness compressibility of the red cell membrane in situ. Pushed into the centers of washed-white red cell ghosts lying on a coverglass, the height of the microsphere-probe tip relative to its closest approach on the adjacent glass surface revealed the apparent material thickness, which began at approximately 90 nm per membrane upon detection of contact (force approximately 1-2 pN). With further impingement, the apparent thickness per membrane diminished over a soft compliant regime that spanned approximately 40 nm and stiffened on approach to approximately 50 nm under forces of approximately 100 pN. The same force-thickness response was obtained on recompression after retraction of the probe, which demonstrated elastic recoverability. Scaled by circumferences of the microspheres, the forces yielded energies of compression per area which exhibited an inverse distance dependence resembling that expected for flexible polymers. Attributed to the spectrin component of the membrane cytoskeleton, the energy density only reached one thermal energy unit (k(B)T) per spectrin tetramer near maximum compression. Hence, we hypothesized that the soft compliant regime probed in the experiments represented the compressibility of the outer region of spectrin loops and that the stiff regime < 50 nm was the response of a compact mesh of spectrin backed by a hardcore structure. To evaluate this hypothesis, we used a random flight theory for the entropic elasticity of polymer loops to model the spectrin network. We also examined the possibility that additional steric repulsion and apparent thickening could arise from membrane thermal-bending excitations. Fixing the energy scale to k(B)T/spectrin tetramer, the combined elastic response of a network of ideal polymer loops plus the membrane steric interaction correlated well with the measured dependence of energy density on distance for a statistical segment length of approximately 5 nm for spectrin (i.e., free chain end-to-end length of approximately 29 nm) and a hardcore limit of approximately 30 nm for underlying structure.     

Importance of matrix permeability and quantity of core habitat for persistence of a threatened saltmarsh bird

Species habitat preferences can be obscured when individuals have been recorded in non‐core habitats because of dispersal, spillover effects or spatial errors in observation locations. Disentangling the direct effects of the habitats species are observed in from the effects of proximity to other nearby habitats is especially challenging in fragmented landscapes, as many fragmentation metrics are correlated and it is difficult to prove independent effects. In this paper we addressed this issue by comparing a number of models based on predefined ecological theories. We compared models based on quantity of core habitat surrounding observations, proximity to core habitat, or a combination of the two to explain the observed distribution of the saltmarsh inhabiting white‐fronted chat (Epthianura albifrons) in coastal New South Wales, Australia. Proximity to core habitat was considered as either Euclidean distance or cost distance, and models were assessed using Akaike's information criterion and the area under the receiver operator characteristic curve on 10 random subsets of the data. We found that all models performed similarly, with the combination of cost distance and the quantity of saltmarsh performing better, but not significantly so. We compared the advantages and disadvantages of different models and also present a model averaged result. Our models suggested that the majority of saltmarshes in New South Wales were too small to have a large effect on probability of occurrence. As climate change is expected to further reduce the amount of available saltmarsh through continued mangrove incursion, coastal populations of the white‐fronted chat are expected to come under increasing threat. The conversion of grasslands to urban areas may also increase the effective distance between different populations of the species and reduce gene flow and rescue effects.     

The Length and Viscosity Dependence of End-to-End Collision Rates in Single-Stranded DNA

Intramolecular dynamics play an essential role in the folding and function of biomolecules and, increasingly, in the operation of many biomimetic technologies. Thus motivated we have employed both experiment and simulation to characterize the end-to-end collision dynamics of unstructured, single-stranded DNAs ranging from 6 to 26 bases. We find that, because of the size and flexibility of the optical reporters employed experimentally, end-to-end collision dynamics exhibit little length dependence at length scales <11 bases. For longer constructs, however, the end-to-end collision rate exhibits a power-law relationship to polymer length with an exponent of −3.49 ± 0.13. This represents a significantly stronger length dependence than observed experimentally for unstructured polypeptides or predicted by polymer scaling arguments. Simulations indicate, however, that the larger exponent stems from electrostatic effects that become important over the rather short length scale of these highly charged polymers. Finally, we have found that the end-to-end collision rate also depends linearly on solvent viscosity, with an experimentally significant, nonzero intercept (the extrapolated rate at zero viscosity) that is independent of chain length—an observation that sheds new light on the origins of the “internal friction” observed in the dynamics of many polymer systems.     

Proximity and grooming patterns reveal opposite-sex bonding in Rwenzori Angolan colobus monkeys (<Emphasis Type="Italic">Colobus angolensis ruwenzorii</Emphasis>)

Close proximity and social grooming are important bonding mechanisms in primates. These behaviors show the social structure of a species and many studies have found positive correlations between the degree of kinship and grooming and proximity. We used 1 year of data collected via instantaneous scan sampling on a large “supertroop” of Colobus angolensis ruwenzorii at Lake Nabugabo, Uganda, to examine partner preferences for grooming and nearest neighbors in each age-sex class. Little is known about this species, so we based our hypotheses on congeners. Of the five species of black-and-white colobus, data on sex-biased dispersal patterns are available for three (C. guereza, C. vellerosus, and C. polykomos), all of which show male-biased dispersal with occasional female dispersal. We thus predicted that female C. a. ruwenzorii would be more strongly bonded than males, showing greater proximity and grooming. We did not expect bonding between the sexes since congeners do not show this pattern. We found that among adult dyads, males and females were more likely to be found in loose proximity, and to groom, than would be expected given group composition. Conversely, both males and females had relatively weak same-sex relationships. Between the sexes, adult males had higher proximity and grooming indices with adult females without infants than with females with infants. These observations indicate that this subspecies is cross-bonded and that both sexes may disperse. Furthermore, our findings suggest that the social organization and social structure of C. a. ruwenzorii differ greatly from other black-and-white colobus species.     

Structural analysis of hyperperiodic DNA from Caenorhabditis elegans

Several bioinformatics studies have identified an unexpected but remarkably prevalent ~10 bp periodicity of AA/TT dinucleotides (hyperperiodicity) in certain regions of the Caenorhabditis elegans genome. Although the relevant C.elegans DNA segments share certain sequence characteristics with bent DNAs from other sources (e.g. trypanosome mitochondria), the nematode sequences exhibit a much more extensive and defined hyperperiodicity. Given the presence of hyperperiodic structures in a number of critical C.elegans genes, the physical characteristics of hyperperiodic DNA are of considerable interest. In this work, we demonstrate that several hyperperiodic DNA segments from C.elegans exhibit structural anomalies using high-resolution atomic force microscopy (AFM) and gel electrophoresis. Our quantitative analysis of AFM images reveals that hyperperiodic DNA adopts a significantly smaller mean square end-to-end distance, hence a more compact coil structure, compared with non-periodic DNA of similar length. While molecules remain capable of adopting both bent and straight (rod-like) configurations, indicating that their flexibility is still retained, examination of the local curvatures along the DNA contour length reveals that the decreased mean square end-to-end distance can be attributed to the presence of long-scale intrinsic bending in hyperperiodic DNA. Such bending is not detected in non-periodic DNA. Similar studies of shorter, nucleosome-length DNAs that survived micrococcal nuclease digestion show that sequence hyperperiodicity in short segments can likewise induce strong intrinsic bending. It appears, therefore, that regions of the C.elegans genome display a significant correlation between DNA sequence and unusual mechanical properties.     

No evidence for female kin association,indications for extragroup paternity,and sex‐biased dispersal patterns in wild western gorillas

Characterizing animal dispersal patterns and the rational behind individuals’ transfer choices is a long‐standing question of interest in evolutionary biology. In wild western gorillas (Gorilla gorilla), a one‐male polygynous species, previous genetic findings suggested that, when dispersing, females might favor groups with female kin to promote cooperation, resulting in higher‐than‐expected within‐group female relatedness. The extent of male dispersal remains unclear with studies showing conflicting results. To investigate male and female dispersal patterns and extragroup paternity, we analyzed long‐term field observations, including female spatial proximity data, together with genetic data (10 autosomal microsatellites) on individuals from a unique set of four habituated western gorilla groups, and four additional extragroup males (49 individuals in total). The majority of offspring (25 of 27) were sired by the group male. For two offspring, evidence for extragroup paternity was found. Contrarily to previous findings, adult females were not significantly more related within groups than across groups. Consistently, adult female relatedness within groups did not correlate with their spatial proximity inferred from behavioral data. Adult females were similarly related to adult males from their group than from other groups. Using R _ST statistics, we found significant genetic structure and a pattern of isolation by distance, indicating limited dispersal in this species. Comparing relatedness among females and among males revealed that males disperse farer than females, as expected in a polygamous species. Our study on habituated western gorillas shed light on the dispersal dynamics and reproductive behavior of this polygynous species and challenge some of the previous results based on unhabituated groups.     

Detecting spatial aggregation from distance sampling: a probability distribution model of nearest neighbor distance

Spatial point pattern is an important tool for describing the spatial distribution of species in ecology. Negative binomial distribution (NBD) is widely used to model spatial aggregation. In this paper, we derive the probability distribution model of event-to-event nearest neighbor distance (distance from a focal individual to its n-th nearest individual). Compared with the probability distribution model of point-to-event nearest neighbor distance (distance from a randomly distributed sampling point to the n-th nearest individual), the new probability distribution model is more flexible. We propose that spatial aggregation can be detected by fitting this probability distribution model to event-to-event nearest neighbor distances. The performance is evaluated using both simulated and empirical spatial point patterns.     

Proximity Labeling Facilitates Defining the Proteome Neighborhood of Photosystem II Oxygen Evolution Complex in a Model Cyanobacterium

Ascorbate peroxidase (APEX)-based proximity labeling coupled with mass spectrometry has a great potential for spatiotemporal identification of proteins proximal to a protein complex of interest. Using this approach is feasible to define the proteome neighborhood of important protein complexes in a popular photosynthetic model cyanobacterium Synechocystis sp. PCC6803 (hereafter named as Synechocystis). To this end, we developed a robust workflow for APEX2-based proximity labeling in Synechocystis and used the workflow to identify proteins proximal to the photosystem II (PS II) oxygen evolution complex (OEC) through fusion APEX2 with a luminal OEC subunit, PsbO. In total, 38 integral membrane proteins (IMPs) and 93 luminal proteins were identified as proximal to the OEC. A significant portion of these proteins are involved in PS II assembly, maturation, and repair, while the majority of the rest were not previously implicated with PS II. The IMPs include subunits of PS II and cytochrome b₆/f, but not of photosystem I (except for PsaL) and ATP synthases, suggesting that the latter two complexes are spatially separated from the OEC with a distance longer than the APEX2 labeling radius. Besides, the topologies of six IMPs were successfully predicted because their lumen-facing regions exclusively contain potential APEX2 labeling sites. The luminal proteins include 66 proteins with a predicted signal peptide and 57 proteins localized also in periplasm, providing important targets to study the regulation and selectivity of protein translocation. Together, we not only developed a robust workflow for the application of APEX2-based proximity labeling in Synechocystis and showcased the feasibility to define the neighborhood proteome of an important protein complex with a short radius but also discovered a set of the proteins that potentially interact with and regulate PS II structure and function.     

Electric dichroism of poly(riboadenylic acid)

Electric dichroism measurements on poly(A) in low-ionic-strength solution demonstrate that below a molecular weight of 130,000 the double-stranded polymer is hydrodynamically rigid and above that molecular weight becomes increasingly flexible. At 500,000 it is considerably more flexible than DNA of the same molecular weight, with a mean end-to-end distance of about 1150 Å compared to approximately 1600 Å for DNA. The fully extended length for both DNA and poly(A) of this molecular weight is about 2750 Å. It is further shown that the orientation of these polyelectrolytes in an electric field is consistent with theoretical treatments of the counter-ion distribution and a preliminary model based on the additivity of classical valence charge anisotropy and counter-ion polarization is postulated for the orientation mechanism. Single-stranded pol (A) is shown not only to retain its base stacking in the presence of the electric field but to extend the persistent regions of stacked bases so that it attains a rodlike structure very similar to the one in the double-stranded polymer is found to be less than that expected from consideration of the x-ray structure. An explanation for this result is sought in the electric asymmetry of the helical polymer.