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Nucleic acid structure

life science Maturity 9-11 Next article →

Nucleic acids, such as DNA and RNA, are the essential molecules that carry biological information. Their function is determined by their complex shapes, which scientists categorize into four distinct levels of organization. These levels include primary, secondary, tertiary, and quaternary structures. Each level builds upon the previous one, moving from a simple sequence of building blocks to complex three-dimensional arrangements.

DNA structure and bases
DNA structure and bases

The primary structure is the most fundamental level. It consists of a linear sequence of nucleotides linked by phosphodiester bonds. Each nucleotide is composed of three specific parts: a nitrogenous base, a five-carbon sugar, and a phosphate group. The nitrogenous bases are classified into two groups: purines and pyrimidines. Purines include adenine (A) and guanine (G), which have a double-ring structure. Pyrimidines include cytosine (C), thymine (T), and uracil (U), which have a single-ring structure. In DNA, the sugar is deoxyribose, while RNA uses ribose. Thymine is found only in DNA, and uracil is found only in RNA.

DNA-Nucleobases
DNA-Nucleobases

Secondary structure describes how these strands interact with one another. In the DNA double helix, two polynucleotide strands are held together by hydrogen bonds between complementary bases. A purine must always pair with a pyrimidine: guanine pairs with cytosine, and adenine pairs with thymine or uracil. While hydrogen bonds align the strands, stacking interactions between the bases provide stronger stability. These interactions are supported by Van der Waals forces and hydrophobic effects. DNA forms a double helix with two distinct grooves: the major groove and the minor groove.

R-Scape Predicted Secondary Structure of SQ1002 sRNA
R-Scape Predicted Secondary Structure of SQ1002 sRNA

RNA secondary structure differs because RNA is often a single polynucleotide. It can fold back on itself to create various shapes through base pairing. Common elements include helices, bulges, and internal loops. A very frequent shape is the stem-loop, or hairpin loop, where the chain folds back to form a double-stranded "stem" and a single-stranded "loop." RNA can also form complex shapes called pseudoknots. These occur when nucleotides in a hairpin loop pair with bases outside of that stem. This creates a structure with two stems and two loops.

Tertiary structure refers to the specific three-dimensional arrangement of the atoms in space. This level involves large-scale folding of the linear polymer. DNA can exist in several different forms depending on its environment. B-DNA is the most common form found in living cells. It is a narrow, elongated helix that thrives in high water concentrations. A-DNA is shorter and wider, appearing under dehydrating conditions with low water concentrations. There is also Z-DNA, which is a rare, left-handed helix that forms in high salt concentrations.

A-B-Z-DNA Side View
A-B-Z-DNA Side View

Circular DNA molecules exhibit unique tertiary properties known as supercoiling. Because circular DNA is topologically constrained, the strands cannot easily change how many times they wrap around each other. This is measured by the linking number (Lk), which is the sum of twists (Tw) and writhes (Wr). Twists are the number of times the two strands rotate around each other. Writhes are the number of times the helix crosses over itself. In many cells, DNA is negatively supercoiled, which makes it easier for the strands to unwind when needed.

The quaternary structure involves the highest level of organization. This level describes how nucleic acids interact with other types of molecules. A primary example is the formation of chromatin. In this process, DNA interacts with small proteins called histones to organize its structure. Quaternary structure is also seen when multiple separate RNA units come together to form functional complexes, such as those found in a ribosome or a spliceosome.

DNA to Chromatin Formation
DNA to Chromatin Formation
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🖼️ Images & Media (6)
File:DNA-Nucleobases.svg
DNA-Nucleobases.svg
File:Неподвижная структура Холлидея (англ.).svg
Неподвижная структура Холлидея (англ.).svg
File:R-Scape Predicted Secondary Structure of SQ1002 sRNA.png
R-Scape Predicted Secondary Structure of...
File:DNA structure and bases.svg
DNA structure and bases.svg
File:A-B-Z-DNA Side View.png
A-B-Z-DNA Side View.png
File:DNA to Chromatin Formation.jpg
DNA to Chromatin Formation.jpg
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