Water–DNA interactions as studied by X–ray and neutron fibre diffraction

Fuller, W.; Forsyth, V. Trevor; Mahendrasingam, A.

doi:10.1098/rstb.2004.1501

Cited by 66 publications

(59 citation statements)

References 27 publications

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“…Apart from X-ray diffraction [3,4] and multidimensional nuclear magnetic resonance [5,6], vibrational spectroscopy has been applied to identify particular functional groups along with their local interactions and to characterize different helix structures of DNA oligomers in their native aqueous environment [7,8]. The infrared spectra of DNA are highly congested with numerous overlapping absorption bands in the fingerprint range and broad, essentially structureless spectral envelopes in the range between 3100 and 4000 cm À1 .…”

Section: Introductionmentioning

confidence: 99%

Ultrafast dynamics of N–H and O–H stretching excitations in hydrated DNA oligomers

et al. 2009

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Section: Introductionmentioning

confidence: 99%

Ultrafast dynamics of N–H and O–H stretching excitations in hydrated DNA oligomers

et al. 2009

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“…A-DNA is considered to be an inactive conformation state, whereas B-DNA is associated with metabolically active DNA, and Z-DNA has been linked to regulation of DNA transcription and gene expression, perhaps affecting the binding of transcription factors (61). When a cell desiccates, the removal of DNA-stabilizing water molecules forces the native B-DNA to adopt different conformations (62), with GC-poor B-DNA forming metabolically inactive A-DNA and GC-rich B-DNA sequences tending to form Z-DNA (63,64). Furthermore, a positive correlation exists between GC content and the ability of DNA to undergo B→Z conformational transitions in genes of humans and other model vertebrates and plants (24).…”

Section: Advantages Of Gc-rich Grass Genomes Under Seasonally Cold Anmentioning

confidence: 99%

Ecological and evolutionary significance of genomic GC content diversity in monocots

Šmarda

Bureš

Horová

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

287

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Genomic DNA base composition (GC content) is predicted to significantly affect genome functioning and species ecology. Although several hypotheses have been put forward to address the biological impact of GC content variation in microbial and vertebrate organisms, the biological significance of GC content diversity in plants remains unclear because of a lack of sufficiently robust genomic data. Using flow cytometry, we report genomic GC contents for 239 species representing 70 of 78 monocot families and compare them with genomic characters, a suite of life history traits and climatic niche data using phylogeny-based statistics. GC content of monocots varied between 33.6% and 48.9%, with several groups exceeding the GC content known for any other vascular plant group, highlighting their unusual genome architecture and organization. GC content showed a quadratic relationship with genome size, with the decreases in GC content in larger genomes possibly being a consequence of the higher biochemical costs of GC base synthesis. Dramatic decreases in GC content were observed in species with holocentric chromosomes, whereas increased GC content was documented in species able to grow in seasonally cold and/or dry climates, possibly indicating an advantage of GC-rich DNA during cell freezing and desiccation. We also show that genomic adaptations associated with changing GC content might have played a significant role in the evolution of the Earth's contemporary biota, such as the rise of grass-dominated biomes during the mid-Tertiary. One of the major selective advantages of GC-rich DNA is hypothesized to be facilitating more complex gene regulation.plant genome | genome size evolution | Poaceae | phylogenetic regression | geographical stratification D eep insights into the genomic architecture of model plants are rapidly accumulating, especially because of advances being made in high-throughput next generation and third generation sequencing techniques (1). However, the genomic constitution of the vast majority of nonmodel plants still remains unknown (2), impeding our understanding of the relationship between particular genomic architectures and evolutionary fitness in various environments. One of the important qualitative aspects of genomic architecture is the genomic nucleotide composition, which is usually expressed as the proportion of guanine and cytosine bases in the DNA molecule (GC content). In prokaryotes, the GC content is a well-studied and widely used character in taxonomy (3), and numerous studies have shown both the impact of GC content on microbial ecology and the influence of the environment in shaping the DNA base composition of microbial communities (4-7). The DNA base composition is also frequently discussed in relation to the evolution of the isochore structure in humans and other homeothermic (warm-blooded) vertebrates (i.e., birds and mammals) (8-10). In contrast, considerably less attention has been paid to the biological relevance of genomic GC content variation in plants (11), with genomic GC co...

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“…The sample was sealed in a flat aluminum holder, effectively fixing the humidity level, as in other, recent neutron scattering experiments [19]. The sample has been used for diffraction studies and presents a well-defined B-DNA structure, as reported by Langridge et al [20] Arnott et al [21] and more recently Fuller et al [22]. In this concentrated form of DNA, fibres are aligned to within a few degrees which is a requirement of the scattering experiment.…”

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confidence: 99%

Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

et al. 2011

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Quantifying the molecular elasticity of DNA is fundamental to our understanding of its biological functions. Recently different groups, through experiments on tailored DNA samples and numerical models, have reported a range of stretching force constants (0.3 to 3 N=m). However, the most direct, microscopic measurement of DNA stiffness is obtained from the dispersion of its vibrations. A new neutron scattering spectrometer and aligned, wet spun samples have enabled such measurements, which provide the first data of collective excitations of DNA and yield a force constant of 83 N=m. Structural and dynamic order persists unchanged to within 15 K of the melting point of the sample, precluding the formation of bubbles. These findings are supported by large scale phonon and molecular dynamics calculations, which reconcile hard and soft force constants. DOI: 10.1103/PhysRevLett.107.088102 PACS numbers: 87.14.gk, 63.22.Àm, 78.70.Nx, 87.10.Tf DNA stores the genetic code of all living organisms. Its principle biological functions of DNA are therefore transcription and replication. These processes take place in cells where DNA undergoes protein-mediated, mechanical manipulation resulting in folding, coiling and denaturing of the DNA molecule. The elasticity of DNA also underpins cleavage by enzymes [1] and the formation of 'bubbles' of locally denatured zones along the helix [2,3]. Models describing biologically relevant processes depend on the mechanical properties of DNA expressed as parameters, such as the base-pair force constant, which is crucial in the process of denaturing of DNA [4,5]. All measurements of DNA elasticity are therefore important in understanding the biological function of DNA and here we focus on stretching elasticity and the underlying base-pair stacking interaction.Recently considerable progress has been made in measuring the flexibility of the DNA helix although one concern is the extent to which the experimental or theoretical approaches themselves influence the results [6]. From well-defined oligomers of DNA, the stretch-torsion coupling can be obtained via magnetic tweezers and measuring the consequent over-or under-winding of the helix by tracking an attached rotor bead. In the work of Gore et al.[7], a stretching elastic modulus is reported, which equates to an inter base-pair force constant of 3 N=m. Another example of a molecular sculpturing approach involves DNA oligomers capped with gold nanoparticles, which allow the end-to-end distance to be measured by small angle x-ray scattering [8]. This work reported corresponding values 10 times smaller: 0:3 N=m. Similarly, Wiggins et al.[9] extracted bending force constants from single DNA molecule conformations on a substrate. They too found that the corresponding force constants are much smaller on a local length scale than predicted by classical elasticity models. A more theoretical approach [10] uses the well-known melting temperatures of DNA to calculate the flexibility on a local length scale via the Peyrard-Bishop model [11], assuming ...

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Water–DNA interactions as studied by X–ray and neutron fibre diffraction

Cited by 66 publications

References 27 publications

Ultrafast dynamics of N–H and O–H stretching excitations in hydrated DNA oligomers

Ultrafast dynamics of N–H and O–H stretching excitations in hydrated DNA oligomers

Ecological and evolutionary significance of genomic GC content diversity in monocots

Direct Determination of the Base-Pair Force Constant of DNA from the Acoustic Phonon Dispersion of the Double Helix

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