Abstract
An affinity capillary electrophoresis method was developed to determine a binding constant between a peptide nucleic acid (PNA) and a hairpin-structured DNA. A diblock copolymer composed of PNA and polyethylene glycol (PEG) was synthesized as a novel affinity probe. The base sequence of the probe's PNA segment was complementary to a hairpin-structured region of a 60-base single-stranded DNA (ssDNA). Upon applying a voltage, the DNA hairpin migrated slowly compared to a random sequence ssDNA in the presence of the PNA probe. This retardation was induced by strand invasion of the PNA into the DNA hairpin to form a hybridized complex, where the PEG segment received a large amount of hydrodynamic friction during electrophoresis. The binding constant between the PNA probe and the DNA hairpin was easily determined by mobility analysis. This simple method would be potentially beneficial in studying binding behaviors of various artificial nucleotides to natural DNA or RNA.
| Original language | English |
|---|---|
| Pages (from-to) | 5204-5209 |
| Number of pages | 6 |
| Journal | Analytical chemistry |
| Volume | 84 |
| Issue number | 12 |
| DOIs | |
| Publication status | Published - Jun 19 2012 |
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All Science Journal Classification (ASJC) codes
- Analytical Chemistry
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Estimation of binding constants of peptide nucleic acid and secondary-structured DNA by affinity capillary electrophoresis. / Kundu, Lal Mohan; Tsukada, Harumi; Matsuoka, Yukiharu; Kanayama, Naoki; Takarada, Tohru; Maeda, Mizuo.
In: Analytical chemistry, Vol. 84, No. 12, 19.06.2012, p. 5204-5209.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Estimation of binding constants of peptide nucleic acid and secondary-structured DNA by affinity capillary electrophoresis
AU - Kundu, Lal Mohan
AU - Tsukada, Harumi
AU - Matsuoka, Yukiharu
AU - Kanayama, Naoki
AU - Takarada, Tohru
AU - Maeda, Mizuo
PY - 2012/6/19
Y1 - 2012/6/19
N2 - An affinity capillary electrophoresis method was developed to determine a binding constant between a peptide nucleic acid (PNA) and a hairpin-structured DNA. A diblock copolymer composed of PNA and polyethylene glycol (PEG) was synthesized as a novel affinity probe. The base sequence of the probe's PNA segment was complementary to a hairpin-structured region of a 60-base single-stranded DNA (ssDNA). Upon applying a voltage, the DNA hairpin migrated slowly compared to a random sequence ssDNA in the presence of the PNA probe. This retardation was induced by strand invasion of the PNA into the DNA hairpin to form a hybridized complex, where the PEG segment received a large amount of hydrodynamic friction during electrophoresis. The binding constant between the PNA probe and the DNA hairpin was easily determined by mobility analysis. This simple method would be potentially beneficial in studying binding behaviors of various artificial nucleotides to natural DNA or RNA.
AB - An affinity capillary electrophoresis method was developed to determine a binding constant between a peptide nucleic acid (PNA) and a hairpin-structured DNA. A diblock copolymer composed of PNA and polyethylene glycol (PEG) was synthesized as a novel affinity probe. The base sequence of the probe's PNA segment was complementary to a hairpin-structured region of a 60-base single-stranded DNA (ssDNA). Upon applying a voltage, the DNA hairpin migrated slowly compared to a random sequence ssDNA in the presence of the PNA probe. This retardation was induced by strand invasion of the PNA into the DNA hairpin to form a hybridized complex, where the PEG segment received a large amount of hydrodynamic friction during electrophoresis. The binding constant between the PNA probe and the DNA hairpin was easily determined by mobility analysis. This simple method would be potentially beneficial in studying binding behaviors of various artificial nucleotides to natural DNA or RNA.
UR - http://www.scopus.com/inward/record.url?scp=84862552226&partnerID=8YFLogxK
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U2 - 10.1021/ac301025m
DO - 10.1021/ac301025m
M3 - Article
C2 - 22624952
AN - SCOPUS:84862552226
VL - 84
SP - 5204
EP - 5209
JO - Analytical Chemistry
JF - Analytical Chemistry
SN - 0003-2700
IS - 12
ER -