A, B and Z–DNA, Cruciform - structure in DNA

DNA can adopt several different conformations beyond the classic B-DNA form. The most well-known are A-DNA, B-DNA, and Z-DNA, each with distinct structural characteristics. Additionally, certain sequences in DNA can form a cruciform structure under specific conditions.

A-DNA

• Structure: A-DNA is a right-handed double helix like B-DNA, but it is more compact. The helix is shorter and wider, with 11 base pairs per turn, compared to B-DNA's 10.5.
• Backbone: The sugar-phosphate backbone is closer to the helical axis, making the grooves less pronounced. The major groove is deep and narrow, while the minor groove is shallow and broad.
• Helical Diameter: Approximately 23 Å.
• Conditions: A-DNA typically forms under conditions of low humidity or dehydration. It is not as common in living cells but can occur in DNA-RNA hybrids and in regions where DNA is bound to certain proteins.
• Function: Although not prevalent in cells, A-DNA may play a role in DNA-protein interactions and the regulation of gene expression.

B-DNA

• Structure: B-DNA is the most common form of DNA in cells, representing the structure described by Watson and Crick. It is a right-handed helix with 10.5 base pairs per turn.
• Backbone: The sugar-phosphate backbone is farther from the helical axis, making the grooves more pronounced. The major groove is wide and deep, while the minor groove is narrow and shallow.
• Helical Diameter: Approximately 20 Å.
• Conditions: B-DNA forms under physiological conditions, such as normal cellular hydration and salt concentrations.
• Function: B-DNA is the standard form in which genetic information is stored and replicated in living cells. It is the most recognized structure of DNA.

Z-DNA

• Structure: Z-DNA is a left-handed double helix, which twists in the opposite direction of A- and B-DNA. It has 12 base pairs per turn, and its zigzag backbone gives it a distinctive appearance.
• Backbone: The sugar-phosphate backbone forms a zigzag pattern, unlike the smooth helical structure of A- and B-DNA. The major and minor grooves are not as distinct.
• Helical Diameter: Approximately 18 Å.
• Conditions: Z-DNA can form under high salt concentrations, supercoiling, or in sequences rich in alternating purines and pyrimidines (e.g., CG repeats).
• Function: Z-DNA may play a role in gene regulation, DNA repair, and chromatin structure. It is also thought to be involved in the formation of supercoils and may affect the expression of certain genes.

Cruciform DNA Structure

• Structure: A cruciform structure is a type of DNA secondary structure that forms when inverted repeat sequences (palindromic sequences) within a DNA molecule fold back on themselves. This results in a cross-shaped (cruciform) structure with two hairpin loops.
• Formation: Cruciform structures are stabilized by the formation of intra-strand base pairing within the palindromic sequences. They occur more readily in negatively supercoiled DNA, where the unwinding of the double helix can lead to the extrusion of these structures.
• Function: Cruciform structures may be involved in the regulation of gene expression, replication, and recombination. They can also serve as binding sites for certain proteins and may play a role in DNA repair mechanisms. However, if not properly managed, they can lead to genomic instability.

Summary

• A-DNA: Right-handed, more compact, less common, typically forms under dehydrated conditions.
• B-DNA: Right-handed, most common form in cells, the standard helical structure.
• Z-DNA: Left-handed, zigzag backbone, forms under specific conditions, may have regulatory roles.
• Cruciform Structure: Cross-shaped structure formed by palindromic sequences, potentially involved in gene regulation and stability.

These different forms and structures of DNA highlight the molecule's flexibility and its ability to adopt various conformations depending on the environmental conditions and sequences involved.