In vitro evolution of intrinsically bent DNA

Area of Science:

• Molecular Biology
• Biophysics
• Genomics

Background:

• Intrinsically bent or curved DNA fragments exhibit anomalous migration patterns during polyacrylamide gel electrophoresis.
• Understanding DNA sequence-structure relationships is crucial for various molecular biology applications.

Purpose of the Study:

• To select and enrich DNA fragments with anomalous mobility indicative of DNA bending.
• To investigate the relationship between specific DNA sequences and intrinsic DNA bending.
• To identify sequence elements that contribute to DNA bending.

Main Methods:

• Utilized a modified Systematic Evolution of Ligands by Exponential Enrichment (SELEX) procedure to select for bent DNA.
• Subjected an initial population of ~10^12 unique DNA sequences to seven rounds of selection and amplification.
• Cloned and sequenced 30 individual DNA fragments from the enriched population.

Main Results:

• Successfully enriched a population of DNA fragments exhibiting anomalous mobility characteristic of bent DNA.
• Analysis of 30 sequenced clones provided insights into the DNA sequence-bending relationship.
• Confirmed some existing hypotheses regarding DNA bending while challenging others.
• Identified the CA/TG dinucleotide base step as a significant, previously underestimated, factor in DNA bending.

Conclusions:

• The SELEX procedure is effective for isolating DNA fragments with specific structural properties like bending.
• DNA sequence composition, particularly the CA/TG dinucleotide, plays a critical role in determining DNA intrinsic curvature.
• These findings refine our understanding of DNA structure and its implications in molecular processes.