Block-units method for conformational calculations of large nucleic acid chains. I. Block-units approximation of atomic structure and conformational energy of polynucleotides

Biopolymers ◽  
1990 ◽  
Vol 29 (12-13) ◽  
pp. 1503-1518 ◽  
Author(s):  
Yu. N. Vorobjev
Keyword(s):  
Nucleic Acid ◽  
Atomic Structure ◽  
Conformational Energy ◽  
Conformational Calculations

scholarly journals PROTEIN-NUCLEIC ACID INTERFACE (PNAI) INHIBITOR DRUG MOLECULES FOR SARS-COV-2

2020 ◽  
Author(s):  
Hamdullah Khadim Sheikh ◽  
Tanzila Arshad ◽  
Zainab Sher Mohammad ◽  
Iqra Arshad ◽  
Mohtasheemul Hassan
Keyword(s):  
Nucleic Acid ◽  
Binding Energy ◽  
Protease Inhibitors ◽  
Atomic Structure ◽  
Molecular Structures ◽  
Drug Molecules ◽  
Protein Nucleic Acid ◽  
Inhibitor Drug

<p>In this research we used the structure of SARS-CoV-2 related, recently mapped, atomic structure of nsp10/16 proteins for docking with some known drug molecular structures at pH 7 and 5. Chosen molecules were azo -N=N- and -COOH derivatives. It was revealed that the molecules showed good binding energy with nsp10/16 protein at both pH. These molecules can act as protein-nucleic acid interface (PNAI) inhibitor drug molecules. Such molecules can be used in combination with polymerase and protease inhibitors for treatment of SARS-CoV-2. </p>

scholarly journals Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Vasantha Basavalingappa ◽  
Santu Bera ◽  
Bin Xue ◽  
Ido Azuri ◽  
Yiming Tang ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Atomic Structure ◽  
Self Assembly ◽  
Peptide Nucleic Acid ◽  
Supramolecular Assemblies ◽  
New Materials ◽  
Structural Patterns ◽  
Mechanical Rigidity ◽  
Hydrogen Bonded

AbstractThe variety and complexity of DNA-based structures make them attractive candidates for nanotechnology, yet insufficient stability and mechanical rigidity, compared to polyamide-based molecules, limit their application. Here, we combine the advantages of polyamide materials and the structural patterns inspired by nucleic-acids to generate a mechanically rigid fluorenylmethyloxycarbonyl (Fmoc)-guanine peptide nucleic acid (PNA) conjugate with diverse morphology and photoluminescent properties. The assembly possesses a unique atomic structure, with each guanine head of one molecule hydrogen bonded to the Fmoc carbonyl tail of another molecule, generating a non-planar cyclic quartet arrangement. This structure exhibits an average stiffness of 69.6 ± 6.8 N m−1 and Young’s modulus of 17.8 ± 2.5 GPa, higher than any previously reported nucleic acid derived structure. This data suggests that the unique cation-free “basket” formed by the Fmoc-G-PNA conjugate can serve as an attractive component for the design of new materials based on PNA self-assembly for nanotechnology applications.

scholarly journals PROTEIN-NUCLEIC ACID INTERFACE (PNAI) INHIBITOR DRUG MOLECULES FOR SARS-COV-2

2020 ◽  
Author(s):  
Hamdullah Khadim Sheikh ◽  
Tanzila Arshad ◽  
Zainab Sher Mohammad ◽  
Iqra Arshad ◽  
Mohtasheemul Hassan
Keyword(s):  
Nucleic Acid ◽  
Binding Energy ◽  
Protease Inhibitors ◽  
Atomic Structure ◽  
Molecular Structures ◽  
Drug Molecules ◽  
Protein Nucleic Acid ◽  
Inhibitor Drug

<p>In this research we used the structure of SARS-CoV-2 related, recently mapped, atomic structure of nsp10/16 proteins for docking with some known drug molecular structures at pH 7 and 5. Chosen molecules were azo -N=N- and -COOH derivatives. It was revealed that the molecules showed good binding energy with nsp10/16 protein at both pH. These molecules can act as protein-nucleic acid interface (PNAI) inhibitor drug molecules. Such molecules can be used in combination with polymerase and protease inhibitors for treatment of SARS-CoV-2. </p>

Introduction

1978 ◽  
Vol 36 (3) ◽  
pp. 543-544
Author(s):  
W. Bernard
Keyword(s):  
Molecular Weight ◽  
Electron Microscope ◽  
Nucleic Acid ◽  
Gene Mapping ◽  
Molecular Genetics ◽  
Cell Biology ◽  
Gene Activity ◽  
Close Connection ◽  
Basic Information ◽  
Simple Systems

In comparison to many other fields of ultrastructural research in Cell Biology, the successful exploration of genes and gene activity with the electron microscope in higher organisms is a late conquest. Nucleic acid molecules of Prokaryotes could be successfully visualized already since the early sixties, thanks to the Kleinschmidt spreading technique - and much basic information was obtained concerning the shape, length, molecular weight of viral, mitochondrial and chloroplast nucleic acid. Later, additonal methods revealed denaturation profiles, distinction between single and double strandedness and the use of heteroduplexes-led to gene mapping of relatively simple systems carried out in close connection with other methods of molecular genetics.

Infection of Escherichia coli with bacteriophages

1969 ◽  
Vol 27 ◽  
pp. 370-371
Author(s):  
Manfred E. Bayer
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acid ◽  
Cell Surface ◽  
Virus Type ◽  
Infection Process ◽  
Adsorption Site ◽  
The Other ◽  
Specific Receptors ◽  
Bacterial Receptors

The first step in the infection of a bacterium by a virus consists of a collision between cell and bacteriophage. The presence of virus-specific receptors on the cell surface will trigger a number of events leading eventually to release of the phage nucleic acid. The execution of the various "steps" in the infection process varies from one virus-type to the other, depending on the anatomy of the virus. Small viruses like ØX 174 and MS2 adsorb directly with their capsid to the bacterial receptors, while other phages possess attachment organelles of varying complexity. In bacteriophages T3 (Fig. 1) and T7 the small conical processes of their heads point toward the adsorption site; a welldefined baseplate is attached to the head of P22; heads without baseplates are not infective.

Radiation-induced surface decomposition

1983 ◽  
Vol 41 ◽  
pp. 368-369
Author(s):  
M. L. Knotek
Keyword(s):  
Ionizing Radiation ◽  
Atomic Structure ◽  
Chemical Bonding ◽  
Neutral Species ◽  
Radiation Induced ◽  
Physical And Chemical ◽  
Surface Decomposition ◽  
The Relationship ◽  
Electron And Photon ◽  
Surface Bond

Modern surface analysis is based largely upon the use of ionizing radiation to probe the electronic and atomic structure of the surfaces physical and chemical makeup. In many of these studies the ionizing radiation used as the primary probe is found to induce changes in the structure and makeup of the surface, especially when electrons are employed. A number of techniques employ the phenomenon of radiation induced desorption as a means of probing the nature of the surface bond. These include Electron- and Photon-Stimulated Desorption (ESD and PSD) which measure desorbed ionic and neutral species as they leave the surface after the surface has been excited by some incident ionizing particle. There has recently been a great deal of activity in determining the relationship between the nature of chemical bonding and its susceptibility to radiation damage.

Simulated Dark-Field Electron Micrographs of Point Defects and Organometallics

1975 ◽  
Vol 33 ◽  
pp. 200-201
Author(s):  
William Krakow
Keyword(s):  
Electron Micrographs ◽  
Point Defects ◽  
Structure Determination ◽  
Atomic Structure ◽  
Image Interpretation ◽  
Dark Field ◽  
Field Electron ◽  
Dark Field Microscopy ◽  
Dark Field Electron

Tilted beam dark-field microscopy has been applied to atomic structure determination in perfect crystals, several synthesized molecules with heavy atcm markers and in the study of displaced atoms in crystals. Interpretation of this information in terms of atom positions and atom correlations is not straightforward. Therefore, calculated dark-field images can be an invaluable aid in image interpretation.

Nucleic Acid Molecules Prepared by Monolayer Techniques

1972 ◽  
Vol 30 ◽  
pp. 178-179
Author(s):  
Dimitrij Lang
Keyword(s):  
Electron Microscopy ◽  
Standard Deviation ◽  
Nucleic Acid ◽  
Cytochrome C ◽  
Nucleic Acids ◽  
Contour Length ◽  
Sample Standard Deviation ◽  
Molecular Weights ◽  
Length Measurements ◽  
Protein Monolayer

The success of the protein monolayer technique for electron microscopy of individual DNA molecules is based on the prevention of aggregation and orientation of the molecules during drying on specimen grids. DNA adsorbs first to a surface-denatured, insoluble cytochrome c monolayer which is then transferred to grids, without major distortion, by touching. Fig. 1 shows three basic procedures which, modified or not, permit the study of various important properties of nucleic acids, either in concert with other methods or exclusively:1) Molecular weights relative to DNA standards as well as number distributions of molecular weights can be obtained from contour length measurements with a sample standard deviation between 1 and 4%.

Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

1992 ◽  
Vol 50 (1) ◽  
pp. 762-763
Author(s):  
Stephen D. Jett
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Carbon Coated ◽  
Nucleoprotein Complexes ◽  
Mobility Shift Assay ◽  
Protein Nucleic Acid ◽  
Gel Mobility Shift ◽  
Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

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