DNA Structure

Z-DNA is a high energy conformer of B-DNA that forms in vivo during transcription as a result of torsional strain generated by a moving polymerase. An understanding of the biological role of Z-DNA has advanced with the discovery that the RNA editing enzyme double-...

A long-term goal of biomedical research is to decipher how genetic processes influence disease formation. Ubiquitous and advancing microarray technology can measure millions of DNA structural variants (single-nucleotide polymorphisms, or SNPs) and thousands of gene transcripts (RNA expression microarrays) in cells. Both of these information modalities can be brought to bear on disease etiology. This paper develops a Bayesian network-based approach to integrate SNP and expression microarray data. The network models SNP-gene interactions using a phenotype-centric network. Inferring the network consists of two steps: variable selection and network learning. The learned network illustrates how functionally dependent SNPs and genes influence each other, and also serves as a predictor of the phenotype. The application of the proposed method to a pediatric acute lymphoblastic leukemia dataset demonstrates the feasibility of our approach and its impact on biological investigation and clinic...

Petunia has played a central role in transformation research since the earliest reports of plant transformation. It was a key model system when the first definitive accounts of Agrobacterium-mediated transformation and direct DNA transfer unequivocally established the transfer and expression of foreign genes in plants. Petunia subsequently played an important role in elucidating many of the characteristics of plant transformation, including unique sites of insertion, variable expression levels, and modified T-DNA structures among independently derived transformants. It was central in the demonstration of transient expression immediately following co-cultivation and transgene-induced silencing of gene expression, two phenomena currently of great importance in studies of gene function. One of the key reasons for the importance of Petunia in plant transformation research has been the selection for and/or identification of genotypes well suited to growth and regeneration in culture, for example, Petunia Mitchell, for which a simple transformation protocol is described. Agro-infiltration for transient gene expression and the development of intragenic vectors to effect gene transfer without the integration of “foreign” DNA represent recent advancements in Petunia transformation. Ease of transformation, coupled with other favorable biological characteristics, ensure that Petunia will remain a valuable model system for studies of gene function in plants.

One of the important issues in molecular biology is the three-dimensional structure (shape) of proteins and deoxyribonucleic acid (DNA) in solution in the cell and the relationship between structure and function. Ordinarily, protein and DNA structure is determined by X-ray crystallography or electron microscopy. Because of the close packing needed for crystallization and the manipulation required to prepare a specimen for How is DNA wound around the enzyme, and

From material processes to elusive patterns, artists and scientists seek models of explanation (Kemp, 2000). Sometimes illusionally evocative, sometimes rigorously formulaic, and at other times sculpturally bounded, these conceptualizing tools have historically linked art and science. Bring to the fore new technologies, digitally driven, and a vast array of alternative schemes become possibilities. High resolution images of cells, scanned helical DNA structures and synaptic neural connections can presently be viewed in real time. Add to the mix embodied transgenic life forms and fabricated animal models, and our conceptualizing tools expand the possibilities for dimensional invention. The accelerating dynamic between cultural and genetic evolution produces what can be termed a co-evolution between technical knowledge and living matter. And it is this co-evolution between technical expertise and animate matter we term technogenesis. 2 In other terms, technogenesis is the way in which the interactions between technology and biology impact our understanding of how nature exists, or would be, conceived and reconfigured in the future. But how do art practices and the life sciences rely on the efficacy of images? And what part do these images play in the acquisition, comprehension, dissemination and even funding of visual or scientific study? In what ways do images reflect the socio/ economic and cultural conditions of producing knowledge? Located somewhere between illusion, proof and cognitive projection, images, hence, become critical fictions operating within the cultural imaginary. They often traverse contested territories situated elsewhere on the axis between fact and fiction. These visualizing models, ubiquitously employed by artists, scientists, designers, corporate advertisers, journalists and politicians, clarify, mislead, aggrandize, stimulate and document. In brief, they are representations embedded in social structures, policy decisions and commercial ventures. As aesthetic devices such images perform their semiotic function activating thought and emotion by their salient powers of communication and circumscribed belief (Anker, 2004).

Ethidium bromide (EB), acridine orange (AO), methylene blue (MB) and other fluorescent compounds are often used to probe DNA structure in drug–DNA and protein–DNA interactions. They bind nucleic acids via intercalative mode and cause major changes to DNA and RNA structures. The aim of this study was to examine the stability and structural features of calf-thymus DNA complexes with EB, AO and MB in aqueous solution, using constant DNA concentration (12.5 mM) and various pigment/DNA(P) ratios of 1/40, 1/20, 1/10, 1/4 and 1/2. FTIR, UV–visible spectroscopy and isothermal titration calorimetry (ITC) are used to determine the ligand intercalation and external binding modes, the binding constant and the stability of pigment–DNA complexes in aqueous solution. Structural analysis showed major intercalation of EB, AO and MB into polynucleotides G–C and A–T base pairs with minor external binding and overall binding constants of KEB = 6.58 × 104 M−1, KAO = 2.69 × 104 M−1 and KMB = 2.13 ×104 M−1. The overall binding constants estimated by UV–visible spectroscopy are consistent with thermodynamic data obtained by ITC, which showed ΔH(EB) = −13.58 kJ/mol, ΔH(AO) = −14.63 kJ/mol and ΔH(MB) = −13.87 kJ/mol with dissociation constants of KEB = 15 μM, KAO = 36 μM and KMB = 46 μM.

Low-pH-induced DNA structural changes were investigated in the pH range 6.8–2.10 by Raman microspectroscopy. Measurements were carried out on calf thymus DNA in the presence of low concentrations of Mg2+ ions. Vibrational spectra are presented in the wavenumber region 500–1650 cm−1. Large changes in the Raman spectra of calf-thymus DNA were observed on lowering the pH value. These are due to protonation and unstacking of the DNA bases during DNA melting and also to changes in the DNA backbone conformation. The intensities of the Raman bands of guanine (681 cm−1), adenine (728 cm−1), thymine (752 cm−1) and cytosine (785 cm−1), typical of the C2′-endo-anti conformation of B-DNA, are discussed. The B-form marker near 835 cm−1 and the base vibrations in the higher wavenumber region (1200–1680 cm−1) are analysed. Effects of low pH value upon the protonation mechanism of opening AT and changing the protonation of GC base pairs in DNA are discussed. Copyright © 2002 John Wiley & Sons, Ltd.