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RNA Structure Probing
Experimental approaches of determining the structure of nucleic acids, such as RNA and DNA, can be largely classified into biophysical and biochemical methods. Biophysical methods use the fundamental physical properties of molecules for structure determination, including X-ray crystallography, NMR and cryo-EM. Biochemical methods exploit the chemical properties of nucleic acids using specific reagents and conditions to assay the structure of nucleic acids. Such methods may involve chemical probing with specific reagents, or rely on native or analogue chemistry. Different experimental approaches have unique merits and are suitable for different experimental purposes. Biophysical methods X-ray crystallography X-ray crystallography is not common for nucleic acids alone, since neither DNA nor RNA readily form crystals. This is due to the greater degree of intrinsic disorder and dynamism in nucleic acid structures and the negatively charged (deoxy)ribose-phosphate backbones, whic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biomolecular Structure
Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary. The scaffold for this multiscale organization of the molecule arises at the secondary level, where the fundamental structural elements are the molecule's various hydrogen bonds. This leads to several recognizable ''domains'' of protein structure and nucleic acid structure, including such secondary-structure features as alpha helixes and beta sheets for proteins, and hairpin loops, bulges, and internal loops for nucleic acids. The terms ''primary'', ''secondary'', ''tertiary'', and '' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nuclear Overhauser Effect
The nuclear Overhauser effect (NOE) is the transfer of nuclear spin polarization from one population of spin-active nuclei (e.g. 1H, 13C, 15N etc.) to another via cross-relaxation. A phenomenological definition of the NOE in nuclear magnetic resonance spectroscopy (NMR) is the change in the integrated intensity (positive or negative) of one NMR resonance that occurs when another is saturated by irradiation with an RF field. The change in resonance intensity of a nucleus is a consequence of the nucleus being close in space to those directly affected by the RF perturbation. The NOE is particularly important in the assignment of NMR resonances, and the elucidation and confirmation of the structures or configurations of organic and biological molecules. The 1H two-dimensional NOE SpectroscopY (NOESY) experiment and its extensions are important tools to identify stereochemistry of proteins and other biomolecules in solution, whereas in solid form crystal x-ray diffraction typicall ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Negative Stain
In microscopy, negative staining is an established method, often used in diagnostic microscopy, for contrasting a thin specimen with an optically opaque fluid. In this technique, the background is stained, leaving the actual specimen untouched, and thus visible. This contrasts with positive staining, in which the actual specimen is stained. Bright field microscopy For bright-field microscopy, negative staining is typically performed using a black ink fluid such as nigrosin and India ink. The specimen, such as a wet bacterial culture spread on a glass slide, is mixed with the negative stain and allowed to dry. When viewed with the microscope the bacterial cells, and perhaps their spores, appear light against the dark surrounding background. An alternative method has been developed using an ordinary waterproof marking pen to deliver the negative stain. Transmission electron microscopy In the case of transmission electron microscopy, opaqueness to electrons is related to the atom ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transmission Electron Microscopy
Transmission electron microscopy (TEM) is a microscopy technique in which a beam of electrons is transmitted through a specimen to form an image. The specimen is most often an ultrathin section less than 100 nm thick or a suspension on a grid. An image is formed from the interaction of the electrons with the sample as the beam is transmitted through the specimen. The image is then magnified and focused onto an imaging device, such as a fluorescent screen, a layer of photographic film, or a sensor such as a scintillator attached to a charge-coupled device. Transmission electron microscopes are capable of imaging at a significantly higher resolution than light microscopes, owing to the smaller de Broglie wavelength of electrons. This enables the instrument to capture fine detail—even as small as a single column of atoms, which is thousands of times smaller than a resolvable object seen in a light microscope. Transmission electron microscopy is a major analytical method i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Single Particle Reconstruction
Single particle analysis is a group of related computerized image processing techniques used to analyze images from transmission electron microscopy (TEM). These methods were developed to improve and extend the information obtainable from TEM images of particulate samples, typically proteins or other large biological entities such as viruses. Individual images of stained or unstained particles are very noisy, and so hard to interpret. Combining several digitized images of similar particles together gives an image with stronger and more easily interpretable features. An extension of this technique uses single particle methods to build up a three-dimensional reconstruction of the particle. Using cryo-electron microscopy it has become possible to generate reconstructions with sub- nanometer resolution and near-atomic resolution first in the case of highly symmetric viruses, and now in smaller, asymmetric proteins as well. Single particle analysis can also be performed by induced c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dalton (unit)
The dalton or unified atomic mass unit (symbols: Da or u) is a non-SI unit of mass widely used in physics and chemistry. It is defined as of the mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state and at rest. The atomic mass constant, denoted ''m''u, is defined identically, giving . This unit is commonly used in physics and chemistry to express the mass of atomic-scale objects, such as atoms, molecules, and elementary particles, both for discrete instances and multiple types of ensemble averages. For example, an atom of helium-4 has a mass of . This is an intrinsic property of the isotope and all helium-4 atoms have the same mass. Acetylsalicylic acid (aspirin), , has an average mass of approximately . However, there are no acetylsalicylic acid molecules with this mass. The two most common masses of individual acetylsalicylic acid molecules are , having the most common isotopes, and , in which one carbon is carbon-13. The molecular mass ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amorphous Ice
Amorphous ice (non-crystalline or "vitreous" ice) is an amorphous solid form of water. Common ice is a crystalline material wherein the molecules are regularly arranged in a hexagonal lattice, whereas amorphous ice has a lack of long-range order in its molecular arrangement. Amorphous ice is produced either by rapid cooling of liquid water (so the molecules do not have enough time to form a crystal lattice), or by compressing ordinary ice at low temperatures. Although almost all water ice on Earth is the familiar crystalline ice Ih, amorphous ice dominates in the depths of interstellar medium, making this likely the most common structure for H2O in the universe at large. Just as there are many different crystalline forms of ice (currently more than seventeen are known), there are also different forms of amorphous ice, distinguished principally by their densities. Formation The production of amorphous ice hinges on the fast rate of cooling. Liquid water must be cooled to its ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cryo-electron Microscopy
Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample solution is applied to a grid-mesh and plunge-frozen in liquid ethane or a mixture of liquid ethane and propane. While development of the technique began in the 1970s, recent advances in detector technology and software algorithms have allowed for the determination of biomolecular structures at near-atomic resolution. This has attracted wide attention to the approach as an alternative to X-ray crystallography or NMR spectroscopy for macromolecular structure determination without the need for crystallization. In 2017, the Nobel Prize in Chemistry was awarded to Jacques Dubochet, Joachim Frank, and Richard Henderson "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution." ''Nature M ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pseudoknot
__NOTOC__ A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. Prediction and identification The structural configuration of pseudoknots does not lend itself well to bio-computational detection due to its context-sensitivity or "overlapping" nature. The base pairing in pseudoknots is not well nested; that is, base pairs occur that "overlap" one another in sequence position. This makes the presence of pseudoknots in RNA sequences more difficult to predict by the standard method of dynamic programming, which use a recursive scoring system to identify paired stems and consequently, most cannot detect non-nested base pairs. The newer method of stochastic context-free grammars su ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. As an important secondary structure of RNA, it can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA binding proteins, and serve as a substrate for enzymatic reactions. Formation and stability The formation of a stem-loop structure is dependent on the stability of the resulting helix and loop regions. The first prerequisite is the presence of a sequence that can fold back on itself to form a paired double helix. The stability of this helix is determined by its length, the number of mismatches or bulges it co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coaxial Stacking
Nucleic acid tertiary structure is the three-dimensional shape of a nucleic acid polymer. RNA and DNA molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structural motifs that serve as molecular building blocks. Some of the most common motifs for RNA and DNA tertiary structure are described below, but this information is based on a limited number of solved structures. Many more tertiary structural motifs will be revealed as new RNA and DNA molecules are structurally characterized. Helical structures Double helix The double helix is the dominant tertiary structure for biological DNA, and is also a possible structure for RNA. Three DNA conformations are believed to be found in nature, A-DNA, B-DNA, and Z-DNA. The "B" form described by James D. Wats ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Karplus Equation
The Karplus equation, named after Martin Karplus, describes the correlation between 3J-coupling constants and dihedral torsion angles in nuclear magnetic resonance spectroscopy: :J(\phi) = A \cos^2 \phi + B \cos\,\phi + C where ''J'' is the 3''J'' coupling constant, \phi is the dihedral angle, and ''A'', ''B'', and ''C'' are empirically derived parameters whose values depend on the atoms and substituents involved. The relationship may be expressed in a variety of equivalent ways e.g. involving cos2 φ rather than cos 2φ —these lead to different numerical values of ''A'', ''B'', and ''C'' but do not change the nature of the relationship. The relationship is used for 3''J''H,H coupling constants. The superscript "3" indicates that a 1H atom is coupled to another 1H atom three bonds away, via H-C-C-H bonds. (Such hydrogens bonded to neighbouring carbon atoms are termed vicinal). The magnitude of these couplings are generally smallest when the torsion angle is close t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
