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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 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.
From the very early stages of structural studies of DNA by X-ray diffraction and biochemical means, molecular models such as the Watson-Crick nucleic acid double helix model were successfully employed to solve the 'puzzle' of DNA structure, and also find how the latter relates to its key functions in living cells.
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.
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 As matched to Ts and Cs matched to Gs. Image from Mao, 2004. [5]
Hoogsteen pairs have quite different properties from Watson–Crick base pairs.The angle between the two glycosidic bonds (ca. 80° in the A• T pair) is larger and the C1 ′ –C1 ′ distance (ca. 860 pm or 8.6 Å) is smaller than in the regular geometry.
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 ...
For nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants, which test alternative tree topologies dnadist DNA distance method which computes four different distances between species from nucleic acid sequences; distances can then be used in the distance matrix programs protdist