Different Between DNA-A form, DNA-B form, DNA-Z form

Different forms of DNA exist because the molecule can shift its structure when the surrounding conditions is changed. It is the property of DNA to show polymorphism, and this is the reason why B-DNA is not the only form present in cells.

It is observed that the B-form is the common right-handed helix under normal physiological conditions, but when the hydration level becomes low or when ionic strength changes, the helix is pushed into other stable or semi-stable structures. It is the process in which the sugar pucker, base orientation, and backbone geometry are altered due to change in humidity, salt concentration, or torsional stress.

A-DNA is formed in reduced hydration because the ordered water molecules present in the minor groove of B-DNA is lost and the molecule is shifted to C3′-endo type pucker, giving a more compact right-handed form. Z-DNA is formed when negative supercoiling acts on alternating purine-pyrimidine sequences, making the backbone adopt a left-handed zig-zag shape.

These forms are important because DNA sometimes need local structural changes for gene regulation, stabilization of RNA-DNA hybrids, and for reducing torsional strain during transcription and replication. Thus different forms are produced when internal or environmental conditions force the molecule to adjust its conformation for maintaining proper cellular functions.

Main spiral properties of DNA forms.

Different Forms of DNA and Differences

B-form of DNA

• It is the most common and stable form of DNA that occur under normal physiological condition.
• It is a right-handed double helix and the two strands is arranged in antiparallel manner.
• The strands is held together by hydrogen bonding between the complementary bases (A–T and G–C).
• The bases are almost perpendicular to the helical axis and these are placed inside the helix.
• In this form the sugar (deoxyribose) generally remain in C2′-endo conformation.
• The glycosyl angle remain in anti-form which keeps the base away from the sugar–phosphate backbone.
• The diameter of the B-DNA is about 20 Å and it is the moderate width structure.
• One complete turn of the helix has about 10–10.5 base pairs.
• The rise per base pair is about 3.4 Å and the pitch of one full turn is about 34–35 Å.
• It has one major groove and one minor groove. The major groove is wider and it is commonly used by many DNA binding proteins.
• Hydration is important for stability and in this form a hydration spine is formed in the minor groove.
• It is comparatively narrower than A-DNA and slightly wider than Z-DNA.

A-form of DNA

• It is a right-handed double helix but it is shorter and wider compared to the common B–form.
• This form is mainly obtained in dehydrating condition and it is rarely seen under normal physiological condition.
• The repeating unit is one base pair and the helix is more compact along its axis.
• The sugar in A-DNA usually remain in C3′-endo conformation and this conformation appear when the hydration around the DNA is reduced.
• The glycosyl angle remain in anti form which keeps the base away from the backbone.
• The diameter is about 23 Å which is wider than B-DNA.
• One turn of the helix has around 11 base pairs.
• The rise per base pair is shorter and it is about 2.6 Å.
• The pitch of one turn is about 28–29 Å which is less compared to B-form.
• The base pairs are highly inclined (about +19°) and this tilt create a central hole in the helix.
• A high propeller twist (around +18°) is also present in this form.
• The major groove is very deep and narrow.
• The minor groove is shallow and wide.
• This form is also seen in double stranded RNA and in DNA–RNA hybrid molecules.
• Some proteins can induce A-form structure and it also occur during special conditions like viral DNA packaging.

Z-form of DNA

• It is a left-handed double helix and this form is completely different from the common B-form and A-form.
• Z-DNA appear mainly in alternating purine–pyrimidine sequence like d(CG)n and it is generally an unstable high-energy form under normal physiological condition.
• Its formation is supported by negative supercoiling in vivo which help in releasing torsional stress during transcription.
• High salt concentration and some chemical modifications like cytosine methylation can also induce this form.
• Some proteins (Z-DNA binding proteins) can stabilize this structure inside the cell.
• The repeating unit is two base pairs and it produce a zigzag pattern in the sugar–phosphate backbone.
• The zigzag backbone is the main feature and it is formed due to alternating syn and anti glycosyl angles.
• Pyrimidines usually remain in C2′-endo pucker with anti conformation.
• Purines change into C3′-endo pucker and they adopt syn conformation which creates the left-handed twist.
• The diameter is about 18 Å, making it the narrowest form among the three.
• One turn has about 12 base pairs and the rise per base pair is about 3.7 Å.
• The pitch per turn is high and it is about 45–46 Å.
• The base pairs are slightly inclined (about −9°) and they are pushed toward the helix periphery.
• There is almost no propeller twist in this form.
• Z-DNA does not show clear major and minor grooves; instead one deep and narrow groove is present.

Different Between DNA-A form, DNA-B form, DNA-Z form

• A-form is a right-handed helix while B-form is also right-handed, but Z-form is a left-handed helix.
• A-form and B-form has one base pair repeating unit, but Z-form has two base pair repeating unit which create a zigzag backbone.
• A-form is the widest with about 23 Å diameter, B-form has about 20 Å diameter, and Z-form is the narrowest with about 18 Å diameter.
• The rise per base pair is shortest in A-form (about 2.6 Å), moderate in B-form (about 3.4 Å), and longest in Z-form (about 3.7 Å).
• One helical turn contain about 11 base pairs in A-form, 10–10.5 base pairs in B-form, and 12 base pairs in Z-form.
• The base pairs in A-form are highly tilted (about +19°), in B-form they are almost perpendicular, and in Z-form they are inclined around −9°.
• A-form uses C3′-endo sugar pucker, B-form uses C2′-endo, while Z-form alternates between C2′-endo in pyrimidines and C3′-endo in purines.
• A-form and B-form have anti glycosyl angle in all bases, but Z-form has alternating anti (pyrimidine) and syn (purine) conformation.
• In A-form the major groove is deep and narrow and the minor groove is shallow.
• In B-form the major groove is wider and easy for protein binding and the minor groove is moderate.
• In Z-form only one deep narrow groove is present because of the zigzag backbone.
• A-form is usually seen under dehydrated condition or in dsRNA and RNA–DNA hybrids.
• B-form is the normal physiological structure of DNA under hydrated condition.
• Z-form is formed under high torsional stress, high salt concentration, or in alternating GC-rich sequences.

Functions of A-form of DNA

• It is the structural form that help in stabilizing DNA under dehydrated condition when the normal B-form cannot remain stable.
• It is the common helical pattern for double stranded RNA (dsRNA) and RNA–DNA hybrid molecules which occur during transcription.
• It helps in proper base pairing in these RNA-involved structures because the C3′-endo sugar pucker is suitable for RNA.
• It is used in protecting DNA inside bacterial spores where some proteins induce A-form and this help in resisting UV damage.
• It may take part in special packaging of viral DNA where the shorter A-form is used as a compressed intermediate.
• It assists in maintaining structural integrity of nucleic acids during low hydration and crystal formation conditions.

Functions of B-form of DNA

• It is the normal and most stable form of DNA that occur under physiological condition.
• This form helps in accurate storage of genetic information because the bases remain almost perpendicular inside the helix.
• It is suitable for replication as the major and minor grooves allow enzymes to identify the bases easily.
• It support transcription because many DNA binding proteins recognize the wider major groove of B-DNA.
• The regular helical structure help in proper base pairing and maintaining the complementary strands.
• It also help in maintaining hydration around the DNA, as B-form is stabilized by a hydration spine mainly in the minor groove.

Functions of Z-form of DNA

• It help in releasing torsional stress created during transcription because the left-handed form can relax negative supercoils.
• It acts as a structural switch that occur in alternating purine–pyrimidine regions and help in regulating gene expression.
• Some proteins specifically bind to Z-DNA and this binding help in signaling pathways and immune responses in the cell.
• It may assist in protecting genome stability by absorbing mechanical strain generated during replication.
• It is involved in certain chromatin remodeling events where a temporary shift from B-form to Z-form is required.
• It help in marking some regulatory DNA segments, especially GC-rich regions, during active transcription.

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