title: RNA intrusions change DNA elastic properties and structure.
abstract: The units of RNA, termed ribonucleoside monophosphates (rNMPs), have been recently found as the most abundant defects present in DNA. Despite the relevance, it is largely unknown if and how rNMPs embedded in DNA can change the DNA structure and mechanical properties. Here, we report that rNMPs incorporated in DNA can change the elastic properties of DNA. Atomic force microscopy (AFM)-based single molecule elasticity measurements show that rNMP intrusions in short DNA duplexes can decrease--by 32%--or slightly increase the stretch modulus of DNA molecules for two sequences reported in this study. Molecular dynamics simulations and nuclear magnetic resonance spectroscopy identify a series of significant local structural alterations of DNA containing embedded rNMPs, especially at the rNMPs and nucleotide 3' to the rNMP sites. The demonstrated ability of rNMPs to locally alter DNA mechanical properties and structure may help in understanding how such intrusions impact DNA biological functions and find applications in structural DNA and RNA nanotechnology.
authors.affiliation: School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. elisa.riedo@physics.gatech.edu.
authors.forename: Hsiang-Chih
authors.initials: HC
authors.lastname: Chiu
authors.forename: Kyung Duk
authors.initials: KD
authors.lastname: Koh
authors.forename: Marina
authors.initials: M
authors.lastname: Evich
authors.forename: Annie L
authors.initials: AL
authors.lastname: Lesiak
authors.forename: Markus W
authors.initials: MW
authors.lastname: Germann
authors.forename: Angelo
authors.initials: A
authors.lastname: Bongiorno
authors.forename: Elisa
authors.initials: E
authors.lastname: Riedo
authors.forename: Francesca
authors.initials: F
authors.lastname: Storici
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D055119:Elastic Modulus; D018625:Microscopy, Atomic Force / Q000379:methods*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012265:Ribonucleotides / Q000737:chemistry*; D013314:Stress, Mechanical
chemical_list: D012265:Ribonucleotides; D004247:DNA