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Visualizing Poloidal Orientation in DNA Minicircles.

作者信息

Lemos Tony, Kim Harold D

机构信息

School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430, USA.

出版信息

bioRxiv. 2025 Aug 20:2025.08.20.671369. doi: 10.1101/2025.08.20.671369.


DOI:10.1101/2025.08.20.671369
PMID:40894713
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12393517/
Abstract

A short (<150 bp) double-stranded DNA (dsDNA) molecule ligated end-to-end forms a DNA minicircle. Due to sequence-dependent, nonuniform bending energetics, such a minicircle is predicted to adopt a certain inside-out orientation, known as the poloidal orientation. Despite theoretical and computational predictions, experimental evidence for this phenomenon has been lacking. In this study, we introduce a single-molecule approach to visualize the poloidal orientation of DNA minicircles. We constructed a set of DNA minicircles, each containing a single biotin located at a different position along one helical turn of the dsDNA, and imaged the location of biotin-bound NeutrAvidin relative to the DNA minicircle using atomic force microscopy (AFM). We applied this approach to two DNA sequences previously predicted to exhibit strongly preferred poloidal orientations. The observed relative positions of NeutrAvidin shifted between the inside and outside of the minicircle with different phases, indicating distinct poloidal orientations for the two sequences. Coarse-grained simulations revealed narrowly distributed poloidal orientations with different mean orientations for each sequence, consistent with the AFM results. Together, our findings provide experimental confirmation of preferred poloidal orientations in DNA minicircles, offering insights into the intrinsic dynamics of circular DNA.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/fc3d186d245d/nihpp-2025.08.20.671369v1-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/9d5440772783/nihpp-2025.08.20.671369v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/9cde3b57cb99/nihpp-2025.08.20.671369v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/15cbdfc8ff22/nihpp-2025.08.20.671369v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/4b82d7290692/nihpp-2025.08.20.671369v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/cdd4ea50cc8a/nihpp-2025.08.20.671369v1-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/fc3d186d245d/nihpp-2025.08.20.671369v1-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/9d5440772783/nihpp-2025.08.20.671369v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/9cde3b57cb99/nihpp-2025.08.20.671369v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/15cbdfc8ff22/nihpp-2025.08.20.671369v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/4b82d7290692/nihpp-2025.08.20.671369v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/cdd4ea50cc8a/nihpp-2025.08.20.671369v1-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d876/12393517/fc3d186d245d/nihpp-2025.08.20.671369v1-f0006.jpg

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本文引用的文献

[1]
Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search.

Nucleic Acids Res. 2025-7-19

[2]
Structure and dynamics of double-stranded DNA rotaxanes.

Nanoscale. 2024-2-22

[3]
How do molecular motors fold the genome?

Science. 2023-11-10

[4]
The impact of the sequence-dependent physical properties of DNA on chromatin dynamics.

Curr Opin Struct Biol. 2023-12

[5]
Spectral analysis of DNA superhelical dynamics from molecular minicircle simulations.

J Chem Phys. 2023-9-14

[6]
Weak tension accelerates hybridization and dehybridization of short oligonucleotides.

Nucleic Acids Res. 2023-4-24

[7]
DeepBend: An interpretable model of DNA bendability.

iScience. 2023-1-7

[8]
DNA minicircles as novel STAT3 decoy oligodeoxynucleotides endowed with anticancer activity in triple-negative breast cancer.

Mol Ther Nucleic Acids. 2022-6-22

[9]
Atomic Force Microscopy of DNA and DNA-Protein Interactions.

Methods Mol Biol. 2022

[10]
Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.

J Chem Theory Comput. 2022-5-10

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