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The nucleic acid notation currently in use was first formalized by the International Union of Pure and Applied Chemistry (IUPAC) in 1970. [1] This universally accepted notation uses the Roman characters G, C, A, and T, to represent the four nucleotides commonly found in deoxyribonucleic acids (DNA).
Nucleic acid design can be used to create nucleic acid complexes with complicated secondary structures such as this four-arm junction. These four strands associate into this structure because it maximizes the number of correct base pairs, with A's matched to T's and C's matched to G's.
The Nussinov-Jacobson [3] algorithm is used to predict secondary structures and also to identify certain design criteria that reduce the possibility of secondary structure formation in a codeword. In essence this algorithm shows how the presence of a cyclic structure in a DNA code reduces the complexity of the problem of testing the codewords ...
The second table, appropriately called the inverse, does the opposite: it can be used to deduce a possible triplet code if the amino acid is known. As multiple codons can code for the same amino acid, the International Union of Pure and Applied Chemistry's (IUPAC) nucleic acid notation is given in some instances.
The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. [1] Jobs can be run online on the NUPACK webserver or NUPACK source code can be downloaded and compiled locally for non-commercial academic use. [2] NUPACK algorithms are formulated in terms of nucleic acid secondary structure.
This is the standard genetic code (NCBI table 1), in amino acid→codon form. By default it is the DNA code; for the RNA code (using Uracil rather than Thymine), add template parameter "T=U". Also listed are the compressed codon forme, using IUPAC nucleic acid notation. It's referenced in a couple of places, so have a single master copy.
Nucleic acids RNA (left) and DNA (right). Nucleic acids are large biomolecules that are crucial in all cells and viruses. [1] They are composed of nucleotides, which are the monomer components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid ...
A sequence begins with a greater-than character (">") followed by a description of the sequence (all in a single line). The lines immediately following the description line are the sequence representation, with one letter per amino acid or nucleic acid, and are typically no more than 80 characters in length. For example: