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Nucleic acid secondary structure is generally divided into helices (contiguous base pairs), and various kinds of loops (unpaired nucleotides surrounded by helices). Frequently these elements, or combinations of them, are further classified into additional categories including, for example, tetraloops , pseudoknots , and stem-loops .
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.
The ViennaRNA Package is software, a set of standalone programs and libraries used for predicting and analysing RNA nucleic acid secondary structures. [1] The source code for the package is released as free and open-source software and compiled binaries are available for the operating systems Linux, macOS, and Windows.
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]
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 ...
Stem-loops are nucleic acid 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 complementary in nucleotide sequence, base-pair to form a double helix that ends ...
The primary structure of a protein is reported starting from the amino N-terminus to the carboxyl C-terminus, while the primary structure of DNA or RNA molecule is known as the nucleic acid sequence reported from the 5' end to the 3' end. The nucleic acid sequence refers to the exact sequence of nucleotides that comprise the whole molecule.
Antisense therapy is the process by which synthesized strands of nucleic acids are used to bind directly and specifically to the mRNA produced by a certain gene, which will inactivate it. Antisense oligonucleotides (ASOs) are commonly used to target C9orf72 RNA of the G-quadruplex GGGGCC expansion repeat region, which has lowered the toxicity ...