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Nucleotide Analog Interference Mapping
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, whi ... [...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 ''q ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Two-dimensional NMR
Two-Dimensional Nuclear Magnetic Resonance (2D NMR) is an advanced spectroscopic technique that builds upon the capabilities of one-dimensional (1D) NMR by incorporating an additional frequency dimension. This extension allows for a more comprehensive analysis of molecular structures. In 2D NMR, signals are distributed across two frequency axes, providing improved resolution and separation of overlapping peaks, particularly beneficial for studying complex molecules. This technique identifies correlations between different nuclei within a molecule, facilitating the determination of connectivity, spatial proximity, and dynamic interactions. 2D NMR encompasses a variety of experiments, including COSY (Correlation Spectroscopy), TOCSY (Total Correlation Spectroscopy), NOESY (Nuclear Overhauser Effect Spectroscopy), and HSQC (Heteronuclear Single Quantum Coherence). These techniques are indispensable in fields such as structural biology, where they are pivotal in determining protein ... [...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 detector such as a scintillator attached to a charge-coupled device or a direct electron detector. 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 micr ... [...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, making interpretation difficult. 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 indu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dalton (unit)
The dalton or unified atomic mass unit (symbols: Da or u, respectively) is a unit of mass defined as of the mass of an Bound state, unbound neutral atom of carbon-12 in its nuclear and electronic ground state and invariant mass, at rest. It is a Non-SI units mentioned in the SI, non-SI unit accepted for use with SI. The word "unified" emphasizes that the definition was accepted by both IUPAP and IUPAC. The atomic mass constant, denoted , is defined identically. Expressed in terms of , the atomic mass of carbon-12: . Its value in International System of Units, SI units is an experimentally determined quantity. The 2022 CODATA recommended value of the atomic mass constant expressed in the SI base unit kilogram is:This value serves as a Conversion of units, conversion factor of mass from daltons to kilograms, which can easily be converted to Gram, grams and other metric units of mass. The 2019 revision of the SI redefined the kilogram by fixing the value of the Planck constant (), i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amorphous Ice
Variations in pressure and temperature give rise to different phases of ice, which have varying properties and molecular geometries. Currently, twenty-one phases, including both crystalline and amorphous ices have been observed. In modern history, phases have been discovered through scientific research with various techniques including pressurization, force application, nucleation agents, and others. On Earth, most ice is found in the hexagonal Ice Ih phase. Less common phases may be found in the atmosphere and underground due to more extreme pressures and temperatures. Some phases are manufactured by humans for nano scale uses due to their properties. In space, amorphous ice is the most common form as confirmed by observation. Thus, it is theorized to be the most common phase in the universe. Various other phases could be found naturally in astronomical objects. Theory Most liquids under increased pressure freeze at ''higher'' temperatures because the pressure helps to hold ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cryo-electron Microscopy
Cryogenic electron microscopy (cryo-EM) is a transmission electron microscopy technique applied to 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 in the structural biology field. 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 Methods'' also named cryo- ... [...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. These structures are categorized as cross (X) topology within the circuit topology framework, which, in contrast to knot theory, is a contact-based approach. 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 recur ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stem-loop
Stem-loops are nucleic acid Biomolecular structure, secondary structural elements which form via intramolecular base pairing in single-stranded DNA or RNA. They are also referred to as hairpins or hairpin loops. A stem-loop occurs when two regions of the same nucleic acid strand, usually Complementarity (molecular biology), complementary in nucleotide sequence, base-pair to form a double helix that ends in a loop of unpaired nucleotides. Stem-loops are most commonly found in RNA, and are a key building block of many RNA biomolecular structure#Secondary structure, secondary structures. Stem-loops can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA-binding protein, RNA binding proteins, and serve as a Substrate (chemistry), substrate for Enzyme catalysis, enzymatic reactions. Formation and stability The formation of a stem-loop is dependent on the stability of the helix and loop regions. The first prerequisite is the p ... [...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. Wat ... [...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 angle, 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 cos 2φ rather than cos2 φ —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 H atoms bonded to neighbouring carbon atoms are termed Vicinal (chemistry), vicinal). The magnitude of these couplings are generally smallest w ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
