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Condensation prevails over B-A transition in the structure of DNA at low humidity.

ABSTRACT: B-A transition and DNA condensation are processes regulated by base sequence and water activity. The constraints imposed by interhelical interactions in condensation compromise the observation of the mechanism by which B and A base-stacking modes influence the global state of the molecule. We used a single-molecule approach to prevent aggregation and mechanical force to control the intramolecular chain association involved in condensation. Force-extension experiments with optical tweezers revealed that DNA stretches as B-DNA under ethanol and spermine concentrations that favor the A-form. Moreover, we found no contour-length change compatible with a cooperative transition between the A and B forms within the intrinsic-force regime. Experiments performed at constant force in the entropic-force regime with magnetic tweezers similarly did not show a bistable contraction of the molecules that could be attributed to the B-A transition when the physiological buffer was replaced by a water-ethanol mixture. A total, stepwise collapse was found instead, which is characteristic of DNA condensation. Therefore, a low-humidity-induced change from the B- to the A-form base-stacking alone does not lead to a contour-length shortening. These results support a mechanism for the B-A transition in which low-humidity conditions locally change the base-stacking arrangement and globally induce DNA condensation, an effect that may eventually stabilize a molecular contour-length reduction.

SUBMITTER: Hormeno S

PROVIDER: S-EPMC3077702 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

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Condensation prevails over B-A transition in the structure of DNA at low humidity.

Hormeño Silvia S Moreno-Herrero Fernando F Ibarra Borja B Carrascosa José L JL Valpuesta José M JM Arias-Gonzalez J Ricardo JR

Biophysical journal 20110401 8

B-A transition and DNA condensation are processes regulated by base sequence and water activity. The constraints imposed by interhelical interactions in condensation compromise the observation of the mechanism by which B and A base-stacking modes influence the global state of the molecule. We used a single-molecule approach to prevent aggregation and mechanical force to control the intramolecular chain association involved in condensation. Force-extension experiments with optical tweezers reveal ...[more]

PMID: 21504737

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Project description:Coastal human-made structures, such as marinas and harbors, are expanding worldwide. Species assemblages described from these artificial habitats are novel relative to natural reefs, particularly in terms of the abundance of nonindigenous species (NIS). Although these fouling assemblages are clearly distinctive, the ecosystem functioning and species interactions taking place there are little understood. For instance, large predators may influence the fouling community development either directly (feeding on sessile fauna) or indirectly (feeding on small predators associated with these assemblages). In addition, by providing refuges, habitat complexity may modify the outcome of species interactions and the extent of biotic resistance (e.g., by increasing the abundance of niche-specific competitors and predators of NIS). Using experimental settlement panels deployed in the field for 2.5 months, we tested the influence of predation (i.e., caging experiment), artificial structural complexity (i.e., mimics of turf-forming species), and their interactions (i.e., refuge effects) on the development of sessile and mobile fauna in two marinas. In addition, we tested the role of biotic complexity-arising from the habitat-forming species that grew on the panels during the trial-on the richness and abundance of mobile fauna. The effect of predation and artificial habitat complexity was negligible, regardless of assemblage status (i.e., native, cryptogenic, and nonindigenous). Conversely, habitat-forming species and associated epibionts, responsible for biotic complexity, had a significant effect on mobile invertebrates (richness, abundance, and community structure). In particular, the richness and abundance of mobile NIS were positively affected by biotic complexity, with site-dependent relationships. Altogether, our results indicate that biotic complexity prevails over artificial habitat complexity in determining the distribution of mobile species under low predation pressure. Facilitation of native and non-native species thus seems to act upon diversity and community development: This process deserves further consideration in models of biotic resistance to invasion in urban marine habitats.

Project description:BackgroundMale sexually selected vocalisations generally contain both individuality and quality cues that are crucial in intra- as well as inter-sexual communication. As individuality is a fixed feature whereas male phenotypic quality changes with age, individuality and quality cues may be subjected to different selection pressures over time. Individuality (for example, morphology of the vocal apparatus) and quality (for example, body size and dominance status) can both affect the vocal production mechanism, inducing the same components of vocalisations to convey both kinds of information. In this case, do quality-related changes to the acoustic structure of calls induce a modification of vocal cues to identity from year to year? We investigated this question in fallow deer (Dama dama), in which some acoustic parameters of vocalisations (groans) code for both individuality and quality.ResultsWe carried out a longitudinal analysis of groan individuality, examining the effects of age and dominance rank on the acoustic structure of groans of the same males recorded during consecutive years. We found both age- and rank-related changes to groans; the minimum values of the highest formant frequencies and the fundamental frequency increased with the age of males and they decreased when males became more dominant. Both age- and rank-related acoustic parameters contributed to individuality. Male quality changed with age, inducing a change in quality-related parameters and thus, a modification of vocal cues to male individuality between years.ConclusionsThe encoding of individuality and quality information in the same components of vocalisations induces a tradeoff between these two kinds of signals over time. Fallow deer vocalisations are honest signals of quality that are not fixed over time but are modified dynamically according to male quality. As they are more reliable cues to quality than to individuality, they may not be used by conspecifics to recognize a given male from one year to another, but potentially used by both sexes to assess male quality during each breeding season.

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Condensation prevails over B-A transition in the structure of DNA at low humidity.

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Condensation prevails over B-A transition in the structure of DNA at low humidity.

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