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Characterization of foldback sequences in hamster DNA using electron microsocpy

A J Bell, N Hardman

Nucleic Acids Research

|January 1, 1977

Summary

This study characterizes foldback DNA sequences in hamster fibroblasts using electron microscopy. It reveals approximately 42,000 inverted sequences, with 45% forming loops, and challenges previous findings on DNA binding assays.

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Area of Science:

Molecular Biology
Genomics
Cell Biology

Background:

Foldback DNA sequences are structural elements within genomes.
Understanding these sequences is crucial for comprehending genome organization and function.
Previous studies have offered limited insights into the precise nature and abundance of foldback sequences in mammalian DNA.

Purpose of the Study:

To characterize foldback DNA sequences in cultured hamster fibroblast nuclear DNA.
To determine the origin, length, and frequency of these inverted sequences.
To investigate the behavior of foldback DNA during renaturation and hydroxyapatite binding.

Main Methods:

Electron microscopy was employed to visualize DNA structures.
Denatured hamster DNA was allowed to anneal under controlled conditions (Cot1 values).
Hydroxyapatite binding was used to separate renatured DNA duplexes.

Main Results:

Approximately half of the observed structures resulted from inverted sequence annealing (foldback DNA).
The average length of inverted sequences was 0.9 kilobases, with an estimated 42,000 such sequences in the hamster genome.
About 45% of foldback sequences formed loops (mean length 1.74 kilobases), and hydroxyapatite binding showed poor recovery of foldback structures due to preferential duplex enrichment.

Conclusions:

Foldback DNA sequences are a significant feature of the hamster genome.
The study provides quantitative data on the size, frequency, and structural characteristics of these sequences.
Current DNA binding techniques may not accurately represent the abundance of foldback DNA due to methodological biases.

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