Author
Martina Banyay
Bio: Martina Banyay is an academic researcher from Stockholm University. The author has contributed to research in topics: Nucleic acid structure & Oligonucleotide. The author has an hindex of 4, co-authored 4 publications receiving 573 citations.
Papers
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TL;DR: This review presents a compilation and discussion of infrared (IR) bands characteristic of nucleic acids in various conformations, aimed at highlighting specific features that are useful for following major changes in nucleic acid structures.
549 citations
TL;DR: The results suggest the coexistence of two different major sugar puckers within the S-conformational family, with an increased relative contribution of the C2'-endo type of sugar in the methylated sequences.
74 citations
TL;DR: It is demonstrated that SET is a valuable tool for visualization of in situ specimens and can provide important information on the subunit assembly of these macromolecular complexes, and thereby aid in the screening assay process in drug development.
Abstract: We describe a novel three-dimensional (3-D) imaging tool for analysis of protein conformation of in situ samples. Sidec (Sidec Technologies AB, Stockholm, Sweden) electron tomography (SET) uses low-dose electron tomography and a refinement algorithm to reconstruct individual proteins and macromolecular complexes. The approach has successfully reconstructed therapeutic proteins in solution. In this study, we investigate the use of SET to visualize ion channels in cells and tissue samples. SET successfully resolved the volume and structural features of the target complex, showing that it was a tetrameric channel with a central pore. The technology could distinguish and provide 3-D images of the intra- and extracellular domains in the ion channel. In addition, SET was able to show that the channel associates in the form of a tetramer with the four subunits preorganized into dimers. While additional studies using smaller antibody markers are needed to resolve the subunit assembly further, this study demonstrates that SET is a valuable tool for visualization of in situ specimens and can provide important information on the subunit assembly of these macromolecular complexes, and thereby aid in the screening assay process in drug development.
10 citations
TL;DR: Fourier transform infrared spectroscopy is used to investigate a single-stranded RNA oligon nucleotide with known NMR solution structure, constructed to model a five nucleotide bulge, and its two-component oligonucleotide counterpart and displays an overall structural similarity between the two model systems.
7 citations
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TL;DR: Although the optical analogs of 2D NMR do not provide an atomic resolution structure of complex molecules, optical domain multi-dimensional spectroscopy has certain advantages because of the dramatic gain in time resolution possible and the ability to directly observe and quantify the couplings between quantum states involved in molecular dynamical processes.
Abstract: Theoretical descriptions of two-dimensional (2D) vibrational and electronic spectroscopy are presented By using a coupled multi-chromophore model, some examples of 2D spectroscopic studies of peptide solution structure determination and excitation transfer process in electronically coupled multi-chromophore system are discussed A few remarks on perspectives of this research area are given
720 citations
TL;DR: This review presents a compilation and discussion of infrared (IR) bands characteristic of nucleic acids in various conformations, aimed at highlighting specific features that are useful for following major changes in nucleic acid structures.
549 citations
TL;DR: In this paper, the authors introduced asymmetry to the standard symmetric Lorentzian and Gaussian lineshapes by replacing the static width parameter of the symmetric profiles with a smoothly varying function that is wave number dependent.
240 citations
TL;DR: In this paper, the first X-ray structure of a type II antibody was determined by crystallizing the obinutuzumab (GA101) Fab fragment alone and in complex with a CD20 cyclopeptide.
215 citations
TL;DR: It is reported that a B- to A-like DNA conformational change can occur in the nuclei of intact cells in response to dehydration, and this transition is reversible upon rehydration in air-dried cells.
Abstract: The ability to detect DNA conformation in eukaryotic cells is of paramount importance in understanding how some cells retain functionality in response to environmental stress. It is anticipated that the B to A transition might play a role in resistance to DNA damage such as heat, desiccation and toxic damage. To this end, conformational detail about the molecular structure of DNA has been derived primarily from in vitro experiments on extracted or synthetic DNA. Here, we report that a B- to A-like DNA conformational change can occur in the nuclei of intact cells in response to dehydration. This transition is reversible upon rehydration in air-dried cells. By systematically monitoring the dehydration and rehydration of single and double-stranded DNA, RNA, extracted nuclei and three types of eukaryotic cells including chicken erythrocytes, mammalian lymphocytes and cancerous rodent fibroblasts using Fourier transform infrared (FTIR) spectroscopy, we unequivocally assign the important DNA conformation marker bands within these cells. We also demonstrate that by applying FTIR spectroscopy to hydrated samples, the DNA bands become sharper and more intense. This is anticipated to provide a methodology enabling differentiation of cancerous from non-cancerous cells based on the increased DNA content inherent to dysplastic and neoplastic tissue.
192 citations