Mechanical Properties of DNA-like Polymers

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2013 Sep 10

PMID 24013560

Citations 18

Authors

Justin P Peters

Shweta P Yelgaonkar

Seergazhi G Srivatsan

Yitzhak Tor

L James Maher 3rd

Affiliations

Soon will be listed here.

Abstract

The molecular structure of the DNA double helix has been known for 60 years, but we remain surprisingly ignorant of the balance of forces that determine its mechanical properties. The DNA double helix is among the stiffest of all biopolymers, but neither theory nor experiment has provided a coherent understanding of the relative roles of attractive base stacking forces and repulsive electrostatic forces creating this stiffness. To gain insight, we have created a family of double-helical DNA-like polymers where one of the four normal bases is replaced with various cationic, anionic or neutral analogs. We apply DNA ligase-catalyzed cyclization kinetics experiments to measure the bending and twisting flexibilities of these polymers under low salt conditions. Interestingly, we show that these modifications alter DNA bending stiffness by only 20%, but have much stronger (5-fold) effects on twist flexibility. We suggest that rather than modifying DNA stiffness through a mechanism easily interpretable as electrostatic, the more dominant effect of neutral and charged base modifications is their ability to drive transitions to helical conformations different from canonical B-form DNA.

Citing Articles

Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy.

Peters J, Maher Iii L Methods Mol Biol. 2024; 2819:297-340.

PMID: 39028513 DOI: 10.1007/978-1-0716-3930-6_15.

Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility.

Back G, Walther D NAR Genom Bioinform. 2023; 5(4):lqad097.

PMID: 37954573 PMC: 10632188. DOI: 10.1093/nargab/lqad097.

Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases.

Kuprikova N, Ondrus M, Bednarova L, Riopedre-Fernandez M, Slavetinska L, Sykorova V Nucleic Acids Res. 2023; 51(21):11428-11438.

PMID: 37870471 PMC: 10681718. DOI: 10.1093/nar/gkad893.

Nanomechanics of negatively supercoiled diaminopurine-substituted DNA.

Salerno D, Marrano C, Cassina V, Cristofalo M, Shao Q, Finzi L Nucleic Acids Res. 2021; 49(20):11778-11786.

PMID: 34718727 PMC: 8599871. DOI: 10.1093/nar/gkab982.

Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids.

Chen Y, Yang H, Chu J Chem Sci. 2021; 11(19):4969-4979.

PMID: 34122953 PMC: 8159235. DOI: 10.1039/d0sc00480d.

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