Structure of nucleic acids is a big concept in biophysics. Nucleic acid structure is multi-level, multi-complex and unified: Primary, secondary, tertiary and quaternary structures constitute the full spatial conformation and functional basis of the nucleic acid molecule. The structure of nucleic acids does not just inform our knowledge of the nature and physiology of life but it opens up new opportunities for the diagnosis and treatment of disease and drug design.
Primary Structure of Nucleic Acids
Nucleic acid fundamental structure-the number and arrangement of nucleotides in the nucleic acid molecule. That is, the nucleotides are bound by 3’,5’-phosphodiester bonds that form the elementary backbone of the nucleic acid chain. That order and association decides the exact spatial shape and biological activity of the nucleic acid molecule.
Characteristics of Primary Structure Of Nucleic Acid
Sequence of Nucleotides: The main structure of nucleic acids lies mainly in the sequence of nucleotides which is important for the biological activity of the nucleic acid. The DNA sequence, for instance, encodes genetic material; the sequence of RNA is a blueprint for proteins.
Connection Technique: The neighboring nucleotides are bonded to each other via 3’,5’-phosphodiester bonds that provide the chain of nucleic acids with orientation: there is a 5’ end and a 3’ end.
Stability: The nucleic acid primary structure is fairly stable and unaffected by environmental change in terms of sequence and conformation.
Primary Structure of DNA
DNA is a big biological mammoth whose four deoxyribonucleotides (dAMP, dGMP, dCMP and dTMP) are connected by 3’,5’-phosphodiester bonds. DNA molecule is big, usually double-stranded, and sometimes single-stranded. The DNA sequence holds the genetic material of organisms, and is the physical foundation of inheritance and variation.
Primary Structure of RNA
And the ribonucleotide sequence and connection patterns in RNA molecules also resemble the 3’,5’-phosphodiester bond. Single-stranded RNA molecules are the norm, although in some places double-strands (such as the cloverleaf shape of tRNA) exist. There are many functions of RNA in the body, from protein-making to controlling gene expression.
Nucleotides raw materials at BOC Sciences
Secondary Structure of Nucleic Acids
The secondary structure of nucleic acids refers to the local spatial conformation formed by the nucleic acid molecule as it further folds based on a single-stranded backbone.
Secondary Structure of DNA
The secondary structure of DNA is primarily the double helix, which consists of two deoxyribonucleotide strands running in opposite directions but parallel to each other, winding around a common axis to form a double helix. In this structure, the bases are located on the inside of the double helix and pair with each other through hydrogen bonds. Adenine (A) pairs with thymine (T) via two hydrogen bonds, while guanine (G) pairs with cytosine (C) via three hydrogen bonds. This base pairing mechanism gives the DNA molecule high stability and specificity.
The secondary structure of DNA also includes various variants, such as the A-type double helix and the Z-type double helix, which may adopt different conformations under different conditions. In addition, DNA can form more complex secondary structures, such as triple and quadruple helices, which play crucial roles in specific biological processes.
Secondary Structure of RNA
The secondary structure of RNA is relatively more complex, as RNA is typically single-stranded, but local regions can form double-stranded structures such as hairpin loops and stem-loop structures. These local double-stranded regions are formed through base pairing within the RNA chain, similar to the base pairing in DNA. However, because RNA typically contains more uracil (U) than thymine (T), the base pairing in RNA is more often A-U instead of A-T.
The secondary structure of RNA is crucial for its biological functions. For example, the cloverleaf structure of tRNA is a typical RNA secondary structure that enables tRNA to accurately recognize and bind to the corresponding codon on mRNA, thereby participating in protein synthesis. Furthermore, the secondary structure of RNA also influences its stability, interactions with proteins, and its localization and function within the cell.
Tertiary Structure of Nucleic Acids
The tertiary structure of nucleic acids refers to the higher-order structure formed by the further folding of the nucleic acid molecule based on its secondary structure.
Tertiary Structure of DNA
For DNA, its tertiary structure is primarily a higher-level structure formed by the additional twisting and coiling of the double helix, specifically manifested as the supercoiled structure. This supercoiling occurs with the involvement of topoisomerases, allowing DNA to form tightly wound coils within the molecule, thereby further compressing its volume and making its storage in the cell more efficient.
The supercoiled structure of DNA can be considered a manifestation of its tertiary structure. In this structure, the DNA double helix can connect end-to-end and undergo further twisting or coiling, forming a twisted, circular supercoil. This structure not only helps with the compact packaging of DNA within the cell but may also influence processes such as DNA replication, transcription, and repair.
Tertiary Structure of RNA
In addition to DNA, RNA molecules also possess a tertiary structure. Taking tRNA as an example, its tertiary structure forms an inverted L-shape. In the cloverleaf-shaped tRNA, which has a secondary structure, the twisting of the molecule allows unpaired bases on one loop to form hydrogen bonds with complementary bases on another loop, resulting in this specific three-dimensional conformation. This tertiary structure is crucial for the function of tRNA because it ensures that tRNA can accurately recognize and bind to the corresponding codon on mRNA, thereby participating in the process of protein synthesis.
Quaternary Structure of Nucleic Acids
The quaternary structure of nucleic acids refers to the complex spatial conformation formed when nucleic acid molecules interact with other molecules, such as proteins or other nucleic acids. This structure typically involves non-covalent binding between nucleic acid chains and proteins or other molecules, such as hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals forces. In living organisms, the quaternary structure of nucleic acids is crucial for achieving their specific biological functions.
Specifically, the quaternary structure of nucleic acids can include the following situations:
Nucleic Acid-Protein Complexes
This is the most common form of quaternary structure for nucleic acids. For example, in the ribosome, rRNA combines with various proteins to form a complex, which is essential for the protein synthesis process. Additionally, many other types of nucleic acid-protein complexes exist, such as spliceosomes and telomerase, which play vital roles in gene expression regulation, DNA repair, and cell division.
Nucleic Acid-Nucleic Acid Complexes
In some cases, nucleic acid molecules can form complex interacting structures with each other. For example, during DNA replication and transcription, the double-stranded DNA partially unwinds to form single-stranded templates, which enzymes such as RNA polymerase bind to in order to synthesize new nucleic acid chains. There are also interactions such as between tRNA and mRNA, which involve the formation of nucleic acid-nucleic acid complexes.
Specific Spatial Conformations
In addition to interactions with proteins or other nucleic acids, nucleic acid molecules themselves can form specific spatial conformations under certain conditions. For instance, under specific ion concentrations and pH levels, DNA can form supercoiled structures and other higher-order conformations. These structures are important for DNA’s tight packaging and gene expression regulation.
The quaternary structure of nucleic acids is not present in all nucleic acid molecules. In living organisms, different types of nucleic acid molecules have distinct structural characteristics depending on their biological functions. Furthermore, the quaternary structure of nucleic acids is influenced by various factors, such as temperature, pH, and ion strength.