Na An

Publications (6) View all

• Article: Modulation of the current signatures of DNA abasic site adducts in the α-hemolysin ion channel.

  Na An, Henry S White, Cynthia J Burrows
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  ABSTRACT: Electrical current signatures of DNA adducts were investigated during immobilization of strands inside the membrane-bound α-hemolysin ion channel. The current blockages produced by these adducts were found to depend on both size and shape, providing insights into the DNA-protein interactions and the size limitation of bulky adducts to be translocated.
  Chemical Communications 10/2012; · 6.17 Impact Factor
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  Article: Crown ether-electrolyte interactions permit nanopore detection of individual DNA abasic sites in single molecules.

  Na An, Aaron M Fleming, Henry S White, Cynthia J Burrows
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  ABSTRACT: DNA abasic (AP) sites are one of the most frequent lesions in the genome and have a high mutagenic potential if unrepaired. After selective attachment of 2-aminomethyl-18-crown-6 (18c6), individual AP lesions are detected during electrophoretic translocation through the bacterial protein ion channel α-hemolysin (α-HL) embedded in a lipid bilayer. Interactions between 18c6 and Na(+) produce characteristic pulse-like current amplitude signatures that allow the identification of individual AP sites in single molecules of homopolymeric or heteropolymeric DNA sequences. The bulky 18c6-cation complexes also dramatically slow the DNA motion to more easily recordable levels. Further, the behaviors of the AP-18c6 adduct are different with respect to the directionalities of DNA entering the protein channel, and they can be precisely manipulated by altering the cation (Li(+), Na(+) or K(+)) of the electrolyte. This method permits detection of multiple AP lesions per strand, which is unprecedented in other work. Additionally, insights into the thermodynamics and kinetics of 18c6-cation interactions at a single-molecule level are provided by the nanopore measurement.
  Proceedings of the National Academy of Sciences 06/2012; 109(29):11504-9. · 9.68 Impact Factor
• Article: Sequence-specific single-molecule analysis of 8-oxo-7,8-dihydroguanine lesions in DNA based on unzipping kinetics of complementary probes in ion channel recordings.

  Anna E P Schibel, Aaron M Fleming, Qian Jin, Na An, Jin Liu, Charles P Blakemore, Henry S White, Cynthia J Burrows
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  ABSTRACT: Translocation measurements of intact DNA strands with the ion channel α-hemolysin (α-HL) are limited to single-stranded DNA (ssDNA) experiments as the dimensions of the channel prevent double-stranded DNA (dsDNA) translocation; however, if a short oligodeoxynucleotide is used to interrogate a longer ssDNA strand, it is possible to unzip the duplex region when it is captured in the α-HL vestibule, allowing the longer strand to translocate through the α-HL channel. This unzipping process has a characteristic duration based on the stability of the duplex. Here, ion channel recordings are used to detect the presence and relative location of the oxidized damage site 8-oxo-7,8-dihydroguanine (OG) in a sequence-specific manner. OG engages in base pairing to C or A with unique stabilities relative to native base Watson-Crick pairings, and this phenomenon is used here to engineer probe sequences (10-15mers) that, when base-paired with a 65mer sequence of interest, containing either G or OG at a single site, produce characteristic unzipping times that correspond well with the duplex melting temperature (T(m)). Unzipping times also depend on the direction from which the duplex enters the vestibule if the stabilities of leading base pairs at the ends of the duplex are significantly different. It is shown here that the presence of a single DNA lesion can be distinguished from an undamaged sequence and that the relative location of the damage site can be determined based on the duration of duplex unzipping.
  Journal of the American Chemical Society 08/2011; 133(37):14778-84. · 9.91 Impact Factor
• Article: Nanopore detection of 8-oxo-7,8-dihydro-2'-deoxyguanosine in immobilized single-stranded DNA via adduct formation to the DNA damage site.

  Anna E P Schibel, Na An, Qian Jin, Aaron M Fleming, Cynthia J Burrows, Henry S White
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  ABSTRACT: The ability to detect DNA damage within the context of the surrounding sequence is an important goal in medical diagnosis and therapies, but there are no satisfactory methods available to detect a damaged base while providing sequence information. One of the most common base lesions is 8-oxo-7,8-dihydroguanine, which occurs during oxidation of guanine. In the work presented here, we demonstrate the detection of a single oxidative damage site using ion channel nanopore methods employing α-hemolysin. Hydantoin lesions produced from further oxidation of 8-oxo-7,8-dihydroguanine, as well as spirocyclic adducts produced from covalently attaching a primary amine to the spiroiminodihydantoin lesion, were detected by tethering the damaged DNA to streptavidin via a biotin linkage and capturing the DNA inside an α-hemolysin ion channel. Spirocyclic adducts, in both homo- and heteropolymer background single-stranded DNA sequences, produced current blockage levels differing by almost 10% from those of native base current blockage levels. These preliminary studies show the applicability of ion channel recordings not only for DNA sequencing, which has recently received much attention, but also for detecting DNA damage, which will be an important component to any sequencing efforts.
  Journal of the American Chemical Society 12/2010; 132(51):17992-5. · 9.91 Impact Factor
• Article: Electrochemical and spectrometric studies of double-strand calf thymus gland DNA denatured by Al(III) at neutral pH.

  Fuping Zhang, Qing Cao, Jiongjia Cheng, Caihua Zhang, Na An, Shuping Bi
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  ABSTRACT: The interaction between double-strand calf thymus gland DNA (ds-DNA) and Al(III) was studied by using differential pulse voltammetry (DPV) at a hanging mercury drop electrode (HMDE), Raman spectrometry and circular dichroism (CD) spectra. It was shown that at neutral pH ds-DNA did not produce any cathodic peak at the HMDE in the potential window from -550 to -2000 mV vs. SCE. However, in the presence of Al(III), a cathodic peak was generated at about -1660 mV, which is ascribed to a reduction of adenine and cytosine residues of single denatured DNA (sd-DNA). It was concluded that ds-DNA was completely denatured to sd-DNA by Al(III) at a neutral pH. The apparent denaturing kinetic velocity constants of ds-DNA by Al(III) were derived from linear increases of the cathodic peak currents with time. When [Al(III)]x[OH(-)](3) > or = 2 x 10(-26), the precipitation of Al(OH)(3) was observed and identified by the Raman spectrum, and inductively coupled plasma atomic emission spectrometry (ICP-AES). CD spectra showed that the B-type of structure conformations of ds-DNA and related sd-DNA did not change with the increment of Al(III) from 5.0 x 10(-7) to 1.0 x 10(-5) M, but the corresponding absorption strengths increased. The related physiological significances and possible applications of the observations were considered.
  Analytical Sciences 09/2009; 25(8):1019-23. · 1.25 Impact Factor