Atomic force microscopy of long and short double-stranded, single-stranded and triple-stranded nucleic acids

Area of Science:

• Biophysics
• Molecular Biology
• Nanotechnology

Background:

• Atomic force microscopy (AFM) is a powerful tool for visualizing biological molecules at the nanoscale.
• Imaging DNA with AFM is crucial for understanding its structure and interactions.
• Pushing the limits of AFM is necessary to identify various DNA types and optimize imaging conditions.

Purpose of the Study:

• To explore the capabilities of AFM for imaging diverse DNA structures.
• To determine suitable substrates and sample preparation methods for DNA imaging.
• To advance the resolution and reliability of AFM for DNA analysis.

Main Methods:

• Utilized Atomic Force Microscopy (AFM) for high-resolution imaging of DNA molecules.
• Examined DNA samples of varying lengths, including short single-stranded DNA (25-50 bases) and double-stranded DNA (100-200 bp).
• Investigated different DNA types such as poly(A), poly(dA.poly(dT)), poly(dG).poly(dC), lambda DNA, and plasmid DNA on various substrates like mica and oxidized silicon.

Main Results:

• Successfully imaged DNA molecules as short as 25 bases, which appeared globular.
• Observed short double-stranded DNA molecules consistent with A-DNA conformation.
• Characterized poly(A) with varying persistence lengths and identified structures consistent with triple-stranded DNA.
• Clearly imaged entire lambda DNA molecules (approx. 16 microns) and plasmid DNA.

Conclusions:

• AFM is a versatile technique capable of imaging a wide range of DNA structures, from short oligonucleotides to large genomic DNA.
• The study demonstrates AFM's potential for identifying different DNA forms and assessing their structural parameters.
• Optimized AFM imaging conditions enable detailed analysis of DNA at the molecular level.