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Nucleic Acid Design
Nucleic acid design is the process of generating a set of nucleic acid base sequences that will associate into a desired conformation. Nucleic acid design is central to the fields of DNA nanotechnology and DNA computing. It is necessary because there are many possible sequences of nucleic acid strands that will fold into a given secondary structure, but many of these sequences will have undesired additional interactions which must be avoided. In addition, there are many tertiary structure considerations which affect the choice of a secondary structure for a given design. Nucleic acid design has similar goals to protein design: in both, the sequence of monomers is rationally designed to favor the desired folded or associated structure and to disfavor alternate structures. However, nucleic acid design has the advantage of being a much computationally simpler problem, since the simplicity of Watson-Crick base pairing rules leads to simple heuristic methods which yield experim ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleobase
Nucleotide bases (also nucleobases, nitrogenous bases) are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases— adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called ''primary'' or ''canonical''. They function as the fundamental units of the genetic code, with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA. Thymine and uracil are distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings. In addition, some viruses have aminoadenine (Z) instead of adenine. It differs in having an extra amine group, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Energy Minimization
In the field of computational chemistry, energy minimization (also called energy optimization, geometry minimization, or geometry optimization) is the process of finding an arrangement in space of a collection of atoms where, according to some computational model of chemical bonding, the net inter-atomic force on each atom is acceptably close to zero and the position on the potential energy surface (PES) is a stationary point (described later). The collection of atoms might be a single molecule, an ion, a condensed phase, a transition state or even a collection of any of these. The computational model of chemical bonding might, for example, be quantum mechanics. As an example, when optimizing the geometry of a water molecule, one aims to obtain the hydrogen-oxygen bond lengths and the hydrogen-oxygen-hydrogen bond angle which minimize the forces that would otherwise be pulling atoms together or pushing them apart. The motivation for performing a geometry optimization is the phys ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heuristic
A heuristic or heuristic technique (''problem solving'', '' mental shortcut'', ''rule of thumb'') is any approach to problem solving that employs a pragmatic method that is not fully optimized, perfected, or rationalized, but is nevertheless "good enough" as an approximation or attribute substitution. Where finding an optimal solution is impossible or impractical, heuristic methods can be used to speed up the process of finding a satisfactory solution. Heuristics can be mental shortcuts that ease the cognitive load of making a decision. Context Gigerenzer & Gaissmaier (2011) state that sub-sets of ''strategy'' include heuristics, regression analysis, and Bayesian inference. Heuristics are strategies based on rules to generate optimal decisions, like the anchoring effect and utility maximization problem. These strategies depend on using readily accessible, though loosely applicable, information to control problem solving in human beings, machines and abstract i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acids Research
''Nucleic Acids Research'' is an open-access peer-reviewed scientific journal published since 1974 by the Oxford University Press. The journal covers research on nucleic acids, such as DNA and RNA, and related work. According to the ''Journal Citation Reports'', the journal's 2021 impact factor is 19.160. The journal publishes two yearly special issues; the first issue of each year is dedicated to biological databases, published in January since 1993, and the other is devoted to papers describing web-based software resources of value to the biological community (web server A web server is computer software and underlying Computer hardware, hardware that accepts requests via Hypertext Transfer Protocol, HTTP (the network protocol created to distribute web content) or its secure variant HTTPS. A user agent, co ...s), published in July since 2003. Journal Rankings Presented below is a summary of current bibliometric rankings for Nucleic Acids Research based on leading eval ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thermodynamic
Thermodynamics is a branch of physics that deals with heat, work, and temperature, and their relation to energy, entropy, and the physical properties of matter and radiation. The behavior of these quantities is governed by the four laws of thermodynamics, which convey a quantitative description using measurable macroscopic physical quantities but may be explained in terms of microscopic constituents by statistical mechanics. Thermodynamics applies to various topics in science and engineering, especially physical chemistry, biochemistry, chemical engineering, and mechanical engineering, as well as other complex fields such as meteorology. Historically, thermodynamics developed out of a desire to increase the efficiency of early steam engines, particularly through the work of French physicist Sadi Carnot (1824) who believed that engine efficiency was the key that could help France win the Napoleonic Wars. Scots-Irish physicist Lord Kelvin was the first to formulate a concise d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Steric Effects
Steric effects arise from the spatial arrangement of atoms. When atoms come close together there is generally a rise in the energy of the molecule. Steric effects are nonbonding interactions that influence the shape (conformational isomerism, conformation) and chemical reaction, reactivity of ions and molecules. Steric effects complement electronic effects, which dictate the shape and reactivity of molecules. Steric repulsive forces between overlapping electron clouds result in structured groupings of molecules stabilized by the way that opposites attract and like charges repel. Steric hindrance Steric hindrance is a consequence of steric effects. Steric hindrance is the slowing of chemical reactions due to steric bulk. It is usually manifested in ''intermolecular reactions'', whereas discussion of steric effects often focus on ''intramolecular interactions''. Steric hindrance is often exploited to control selectivity, such as slowing unwanted side-reactions. Steric hindran ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid Primary Structure
A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, the sense strand is used. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure. The sequence represents genetic information. Biological deoxyribonucleic acid represents the information which directs the functions of an organism. Nucleic acids also have a secondary structure and tertiary structure. Primary structure is sometimes mistakenly referred to as "primar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Structure
Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary. Primary structure Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bonds. It is this linear sequence of nucleotides that make up the primary structure of DNA or RNA. Nucleotides consist of 3 components: # Nitrogenous base ## Adenine ## Guanine ## Cytosine ## Thymine (present in DNA only) ## Uracil (present in RNA only) # 5-carbon sugar which is called deoxyribose (found in DNA) and ribose (found in RNA). # One or more phosphate groups. The nitrogen bases adenine and guanine are purine in structure and form a glycosidic bond between their 9 nitrogen and the 1' -OH group of the deoxyribose. Cytosine, thymine, and uracil are pyrimidines, hence the glycosidic bonds form between ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Complementarity (molecular Biology)
In molecular biology, complementarity describes a relationship between two structures each following the lock-and-key principle. In nature complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the reverse of things. This complementary base pairing allows cells to copy information from one generation to another and even find and repair damage to the information stored in the sequences. The degree of complementarity between two nucleic acid strands may vary, from complete complementarity (each nucleotide is across from its opposite) to no complementarity (each nucleotide is not across from its opposite) and determines the stability of the sequences to be together. Furthermore, various DNA repair functions as well as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Double Helix
In molecular biology, the term double helix refers to the structure formed by base pair, double-stranded molecules of nucleic acids such as DNA. The double Helix, helical structure of a nucleic acid complex arises as a consequence of its Nucleic acid secondary structure, secondary structure, and is a fundamental component in determining its Nucleic acid tertiary structure, tertiary structure. The structure was discovered by Rosalind Franklin and her student Raymond Gosling, Maurice Wilkins, James Watson, and Francis Crick, while the term "double helix" entered popular culture with the 1968 publication of Watson's ''The Double Helix, The Double Helix: A Personal Account of the Discovery of the Structure of DNA''. The DNA double helix biopolymer of nucleic acid is held together by nucleotides which base pair together. In B-DNA, the most common double helical structure found in nature, the double helix is right-handed with about 10–10.5 base pairs per turn. The double helix struc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thymine
Thymine () (symbol T or Thy) is one of the four nucleotide bases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. In RNA, thymine is replaced by the nucleobase uracil. Thymine was first isolated in 1893 by Albrecht Kossel and Albert Neumann from calf thymus glands, hence its name. Derivation As its alternate name (5-methyluracil) suggests, thymine may be derived by methylation of uracil at the 5th carbon. In RNA, thymine is replaced with uracil in most cases. In DNA, thymine (T) binds to adenine (A) via two hydrogen bonds, thereby stabilizing the nucleic acid structures. Thymine combined with deoxyribose creates the nucleoside deoxythymidine, which is synonymous with the term thymidine. Thymidine can be phosphorylated with up to three phosphoric acid groups, producing dTMP (deoxythymidine monophosphate), dTDP, or dTTP (for the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
