DNA with adenine tracts contains poly(dA).poly(dT) conformational features in solution

Area of Science:

• Molecular Biology
• Biophysics
• Spectroscopy

Background:

• DNA conformation is crucial for its function and interactions.
• Adenine-thymine (AT) rich sequences are known to exhibit unusual structural properties, including DNA bending.
• Electrophoretic mobility retardation is often associated with non-canonical DNA structures.

Purpose of the Study:

• To investigate the solution conformation of DNA multimers containing adenine-thymine tracts.
• To correlate DNA conformation with observed electrophoretic migration anomalies.
• To elucidate the structural basis of DNA bending in AT-rich sequences.

Main Methods:

• Circular Dichroism (CD) spectroscopy to probe DNA secondary structure.
• Raman spectroscopy to analyze the DNA sugar-phosphate backbone.
• Synthesis of specific DNA multimers with varying AT tract lengths and flanking sequences.

Main Results:

• Curved DNA multimers with AT tracts displayed CD spectra indicative of a non-B DNA structure, resembling polyd(A).polyd(T).
• Spectroscopic features suggest the presence of large propeller twists in the adenine bases.
• Raman spectra revealed backbone rearrangements in AT tracts, with unique sugar puckering (C2'-endo/C1'-exo) in multimers compared to polydA.polydT.

Conclusions:

• Adenine-thymine tracts in specific DNA multimers adopt non-B conformations, contributing to altered structural and migratory properties.
• The conformation of AT tracts is influenced by flanking sequences and the interruption by other bases.
• These findings provide insights into the structural diversity of DNA and the factors governing its conformation.