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Kim, Hajin
Single Molecule Biophysics Lab
Research Interests
  • Biophysics, Single Molecule, fluorescence Spectroscopy, biological Motors, biomolecular assembly

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A rule of seven in Watson-Crick base-pairing of mismatched sequences

Cited 24 times inthomson ciCited 18 times inthomson ci
Title
A rule of seven in Watson-Crick base-pairing of mismatched sequences
Author
Cisse, Ibrahim I.Kim, HajinHa, Taekjip
Keywords
RESONANCE ENERGY-TRANSFER; NEAREST-NEIGHBOR THERMODYNAMICS; NUCLEIC-ACID HYBRIDIZATION; TARGET RECOGNITION; DNA; MICRORNAS; KINETICS; IMPACT; OLIGONUCLEOTIDE; SPECTROSCOPY
Issue Date
201206
Publisher
NATURE PUBLISHING GROUP
Citation
NATURE STRUCTURAL & MOLECULAR BIOLOGY, v.19, no.6, pp.623 - +
Abstract
Sequence recognition through base-pairing is essential for DNA repair and gene regulation, but the basic rules governing this process remain elusive. In particular, the kinetics of annealing between two imperfectly matched strands is not well characterized, despite its potential importance in nucleic acid-based biotechnologies and gene silencing. Here we use single-molecule fluorescence to visualize the multiple annealing and melting reactions of two untethered strands inside a porous vesicle, allowing us to precisely quantify the annealing and melting rates. The data as a function of mismatch position suggest that seven contiguous base pairs are needed for rapid annealing of DNA and RNA. This phenomenological rule of seven may underlie the requirement for seven nucleotides of complementarity to seed gene silencing by small noncoding RNA and may help guide performance improvement in DNA- and RNA-based bio- and nanotechnologies, in which off-target effects can be detrimental.
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DOI
http://dx.doi.org/10.1038/nsmb.2294
ISSN
1545-9993
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