ArticleBiochemistry2009
Dynamics and stability of individual base pairs in two homologous RNA-DNA hybrids.
Article in Biochemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 33 citations in OpenAlex.
- Thymine DNA glycosylase binds to R-loops and excises 5-formyl and 5-carboxyl cytosine from DNA/RNA hybrids.The Journal of biological chemistry · 2026Article
- Controlling DNA-RNA strand displacement kinetics with base distribution.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Deaminase-Driven Reverse Transcription Mutagenesis in Oncogenesis: Critical Analysis of Transcriptional Strand Asymmetries of Single Base Substitution Signatures.International journal of molecular sciences · 2025Review
- The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2024Article
- Shedding light on the base-pair opening dynamics of nucleic acids in living human cells.Nature communications · 2022Article
- Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy.iScience · 2022Article
- GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid Duplexes.Biophysical journal · 2020Article
- Structural Flexibility of DNA-RNA Hybrid Duplex: Stretching and Twist-Stretch Coupling.Biophysical journal · 2019Article
- Non-programmed transcriptional frameshifting is common and highly RNA polymerase type-dependent.Microbial cell factories · 2018Article
- Role of nucleotide identity in effective CRISPR target escape mutations.Nucleic acids research · 2018Article
- Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing.RNA biology · 2018Article
- A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation.PLoS computational biology · 2016Article
- Article
- The presence of an RNA:DNA hybrid that is prone to slippage promotes termination by T7 RNA polymerase.Journal of molecular biology · 2014Article
- Bacteriophage λ N protein inhibits transcription slippage by Escherichia coli RNA polymerase.Nucleic acids research · 2014Article
- Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine.Biochemistry · 2013Article
- Characterization of 582 natural and synthetic terminators and quantification of their design constraints.Nature methods · 2013Article
- Direct observation of the temperature-induced melting process of the Salmonella fourU RNA thermometer at base-pair resolution.Nucleic acids research · 2010Article
- Structural energetics of the adenine tract from an intrinsic transcription terminator.Journal of molecular biology · 2010Article
- R loops stimulate genetic instability of CTG.CAG repeats.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Nuclear magnetic resonance spectroscopy and proton exchange have been used to characterize two RNA-DNA hybrids from the tR2 intrinsic transcription terminator site of phage lambda. The hybrids have the same base sequence [5'-GGCGCAGGCC(T/U)(T/U)CC-3'/5'-GGAAGGCC(T/U)GCGCC-3'] but differ from each other by an interchange of DNA and RNA strands. The opening of single base pairs in the two hybrids is characterized by measuring the rates of exchange of imino protons with solvent protons as a function of the concentration of a proton acceptor (ammonia base) at 10 degrees C. The free energy change in the opening reaction provides a measure of the stability of the base pair, while the rates of opening and closing define the base pair dynamics. The results demonstrate that, within the same base sequence context, dA-rU base pairs are less stable than dT-rA base pairs. The differences in stability are enhanced when two dA-rU base pairs are located next to each other in the hybrid structure. For the G-C base pairs, the rates of opening and closing and the stability are affected by the base sequence context and by the nature of the sugar moiety attached to the guanine. The dominant feature of the base sequence is the proximity of the dA-rU base pair, which destabilizes the G-C base pair when the guanine is located on the DNA strand. Two G-C base pairs (namely, those in the fourth and 10th positions) exhibit large differences in their opening and closing rates between the two hybrids, while maintaining the same stability. These results provide the first demonstration that, for RNA-DNA hybrid structures with the same base sequence, the opening dynamics and the stability of individual base pairs are strongly influenced by the chemical nature of each strand.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.