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

Citation data:

Nature structural & molecular biology, ISSN: 1545-9985, Vol: 19, Issue: 6, Page: 623-7

Publication Year:
2012
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Citations 68
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Repository URL:
http://scholarworks.unist.ac.kr/handle/201301/7105
PMID:
22580558
DOI:
10.1038/nsmb.2294
PMCID:
PMC3372693
Author(s):
Cisse, Ibrahim I.; Kim, Hajin; Ha, Taekjip
Publisher(s):
Springer Nature; NATURE PUBLISHING GROUP
Tags:
Biochemistry, Genetics and Molecular Biology; RESONANCE ENERGY-TRANSFER; NEAREST-NEIGHBOR THERMODYNAMICS; NUCLEIC-ACID HYBRIDIZATION; TARGET RECOGNITION; DNA; MICRORNAS; KINETICS; IMPACT; OLIGONUCLEOTIDE; SPECTROSCOPY
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article description
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.