Nucleic acid structure

Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary.

Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bonds.

Cytosine, thymine, and uracil are pyrimidines, hence the glycosidic bonds form between their 1 nitrogen and the 1' -OH of the deoxyribose.

[3] A nucleic acid sequence is the order of nucleotides within a DNA (GACT) or RNA (GACU) molecule that is determined by a series of letters.

[4] There are three potential metal binding groups on nucleic acids: phosphate, sugar, and base moieties.

DNA's secondary structure is predominantly determined by base-pairing of the two polynucleotide strands wrapped around each other to form a double helix.

The four basic elements in the secondary structure of RNA are: The antiparallel strands form a helical shape.

There are three common families of tetraloop in ribosomal RNA: UNCG, GNRA, and CUUG (N is one of the four nucleotides and R is a purine).

[9] Pseudoknot is an RNA secondary structure first identified in turnip yellow mosaic virus.

The main points in the DotKnot-PW method is scoring the similarities found in stems, secondary elements and H-type pseudoknots.

[12] Tertiary structure refers to the locations of the atoms in three-dimensional space, taking into consideration geometrical and steric constraints.

The tertiary arrangement of DNA's double helix in space includes B-DNA, A-DNA, and Z-DNA.

B-DNA is the most common form of DNA in vivo and is a more narrow, elongated helix than A-DNA.

The sugar pucker which determines the shape of the a-helix, whether the helix will exist in the A-form or in the B-form, occurs at the C2'-endo.

[14] In localized single strand dinucleotide contexts, RNA can also adopt the B-form without pairing to DNA.

[15] A-DNA has a deep, narrow major groove which does not make it easily accessible to proteins.

More recently circular RNA was described as well to be a natural pervasive class of nucleic acids, expressed in many organisms (see CircRNA).

A covalently closed, circular DNA (also known as cccDNA) is topologically constrained as the number of times the chains coiled around one other cannot change.

The linking number for circular DNA can only be changed by breaking of a covalent bond in one of the two strands.

Always an integer, the linking number of a cccDNA is the sum of two components: twists (Tw) and writhes (Wr).