title: Direct, sequence-specific detection of dsDNA based on peptide nucleic acid and graphene oxide without requiring denaturation.
abstract: Sequence-specific detection of double stranded DNA (dsDNA) is important in various research fields. In general, denaturation of dsDNA into single strands is necessary for the sequence-specific recognition of probes to target DNA, posing several drawbacks which decrease the efficiency as a DNA sensor. Herein, we report a direct, sequence-specific dsDNA detection system without requiring any thermal denaturing step. Our strategy utilizes peptide nucleic acid (PNA) and graphene oxide (GO) as a probe and as a fluorescence quencher, respectively. The PNA first binds to the end of dsDNA strand due to the relatively easily dissociable terminal base pairs of DNA duplex. Next, superior binding affinity of PNA towards complementary DNA induces branch migration for gradual strand replacement, resulting in the formation of PNA/DNA duplex. Unlike other dsDNA sensors based on complementary DNA probes, PNA in combination with GO enabled hybridization with the target sequence hidden as a duplex form without denaturing step and thus, the formation of PNA/DNA duplex was translated into selective fluorescence signal. Moreover, it provided tighter turn-on signal control with very low background signal and high sensitivity and sequence selectivity even in the presence of serum proteins.
authors.affiliation: Center for RNA Research, Institute for Basic Science, Seoul National University, Seoul 151-747, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea.
authors.forename: Jieon
authors.initials: J
authors.lastname: Lee
authors.affiliation: Center for RNA Research, Institute for Basic Science, Seoul National University, Seoul 151-747, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea.
authors.forename: Il-Soo
authors.initials: IS
authors.lastname: Park
authors.affiliation: Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
authors.forename: Euihan
authors.initials: E
authors.lastname: Jung
authors.affiliation: Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
authors.forename: Younghoon
authors.initials: Y
authors.lastname: Lee
authors.affiliation: Center for RNA Research, Institute for Basic Science, Seoul National University, Seoul 151-747, Republic of Korea; Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea. Electronic address: dalheemin@snu.ac.kr.
authors.forename: Dal-Hee
authors.initials: DH
authors.lastname: Min
mesh_terms: D001483:Base Sequence; D015374:Biosensing Techniques / Q000379:methods*; D004247:DNA / Q000032:analysis* / Q000235:genetics*; D015342:DNA Probes; D006108:Graphite; D057139:Nanofibers; D009691:Nucleic Acid Denaturation; D020135:Peptide Nucleic Acids
chemical_list: D015342:DNA Probes; D020135:Peptide Nucleic Acids; D006108:Graphite; D004247:DNA
keywords: Biosensor; DNA detection; DNA duplex; FRET; Graphene oxide; Peptide nucleic acid