The Mechanical Properties of RNA-DNA Hybrid Duplex Stretched by Magnetic Tweezers
| Autor: | Er-Chi Zhou, Ya-Jun Yang, Xing-Hua Zhang, Zhi-Jie Tan, Huijuan You, Hang Fu, Chen Zhang |
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| Rok vydání: | 2019 |
| Předmět: |
Persistence length
0303 health sciences Magnetic tweezers Nucleic Acid Heteroduplexes Biophysics RNA DNA Articles 03 medical and health sciences chemistry.chemical_compound Magnetic Fields 0302 clinical medicine chemistry Duplex (building) Reannealing Nucleic acid Mammalian genome R-Loop Structures 030217 neurology & neurosurgery Mechanical Phenomena 030304 developmental biology |
| Zdroj: | Biophysical Journal. 116:196-204 |
| ISSN: | 0006-3495 |
| DOI: | 10.1016/j.bpj.2018.12.005 |
| Popis: | RNA can anneal to its DNA template to generate an RNA-DNA hybrid (RDH) duplex and a displaced DNA strand, termed R-loop. RDH duplex occupies up to 5% of the mammalian genome and plays important roles in many biological processes. The functions of RDH duplex are affected by its mechanical properties, including the elasticity and the conformation transitions. The mechanical properties of RDH duplex, however, are still unclear. In this work, we studied the mechanical properties of RDH duplex using magnetic tweezers in comparison with those of DNA and RNA duplexes with the same sequences. We report that the contour length of RDH duplex is ∼0.30 nm/bp, and the stretching modulus of RDH duplex is ∼660 pN, neither of which is sensitive to NaCl concentration. The persistence length of RDH duplex depends on NaCl concentration, decreasing from ∼63 nm at 1 mM NaCl to ∼49 nm at 500 mM NaCl. Under high tension of ∼60 pN, the end-opened RDH duplex undergoes two distinct overstretching transitions; at high salt in which the basepairs are stable, it undergoes the nonhysteretic transition, leading to a basepaired elongated structure, whereas at low salt, it undergoes a hysteretic peeling transition, leading to the single-stranded DNA strand under force and the single-stranded RNA strand coils. The peeled RDH is difficult to reanneal back to the duplex conformation, which may be due to the secondary structures formed in the coiled single-stranded RNA strand. These results help us understand the full picture of the structures and mechanical properties of nucleic acid duplexes in solution and provide a baseline for studying the interaction of RDH with proteins at the single-molecule level. |
| Databáze: | OpenAIRE |
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