DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum

Area of Science:

• Molecular Biology
• Structural Biology
• Biophysics

Background:

• DNA A-tracts are sequences of four or more adenine-thymine base pairs.
• In-phase A-tracts can cause DNA bending, but the reason for differential bending between A4T4 and T4A4 sequences was unclear.

Purpose of the Study:

• To elucidate the structural basis for the differential bending of A4T4 and T4A4 DNA sequences.
• To understand how DNA sequence influences higher-order DNA structure and properties.

Main Methods:

• Nuclear Magnetic Resonance (NMR) spectroscopy was used to determine the solution structures of A4T4 and T4A4 DNA duplexes.
• Refinement with residual dipolar couplings was employed for structural analysis.
• NMR-based structural modeling was performed on longer DNA sequences.
• Gel electrophoretic mobility studies were conducted.

Main Results:

• The ApT step in A4T4 DNA exhibits a large negative roll, bending toward the minor groove.
• The TpA step in T4A4 DNA has a positive roll, bending toward the major groove.
• A4T4 DNA bends in phase with junctional bends, creating a pronounced minor groove bend and forming a left-handed superhelix.
• T4A4 DNA bends oppose each other, resulting in a straight helix with gentle writhe.
• Higher-order DNA structure and electrophoretic mobility are influenced by monovalent cations.

Conclusions:

• The differential bending of A-tracts is determined by the roll angles at ApT and TpA steps.
• Sequence-dependent DNA bending dictates higher-order structures, such as supercoiling, with implications for DNA packaging.
• Monovalent cations play a role in modulating DNA structure and behavior.