End Of ssDNA Research Articles

Cascade signal amplifying strategy for ultrasensitive detection of tumor biomarker by DNAzyme cleaving mediated HCR

Tumor biomarkers are a kind of important biomolecules for aiding cancer diagnosis and assessing tumor efficacy, among which alpha-fetoprotein (AFP) is a crucial tumor biomarker for the early diagnosis of hepatocellular carcinoma. In this study, a novel cascade signal amplifying strategy was designed for the ultrasensitive detection of AFP by DNAzyme cleaving-mediated hybridization chain reaction (HCR). The primary antibody was immobilized on the Au nanoparticles modified glassy carbon electrode, which subsequently captured AFP and the secondary antibody. Then, streptavidin was combined with the biotin-modified secondary antibody and Cu2+-specific DNAzyme. When Cu2+ was present, the substrate strand of the DNAzyme would cleave and produce an ssDNA end. Finally, HCR was triggered to form long double-stranded DNA on the electrode, which would greatly inhibit the charge transfer at the electrode/solution interface. Therefore, the DNAzyme cleaving-mediated HCR strategy can be applied as cascade signal amplification for the ultrasensitive electrochemical determination of tumor biomarker AFP. Under optimal conditions, the immunosensor exhibits a broad linear range of 0.001−100 ng·mL−1 (R2 = 0.990) and a low detection limit of 15.8 fg·mL−1. The proposed sensor displays high sensitivity and selectivity for AFP detection, which can be employed as a universal sensing platform in clinical diagnostics.

RecA and SSB genome-wide distribution in ssDNA gaps and ends in Escherichia coli.

Single-stranded DNA (ssDNA) gapped regions are common intermediates in DNA transactions. Using a new non-denaturing bisulfite treatment combined with ChIP-seq, abbreviated 'ssGap-seq', we explore RecA and SSB binding to ssDNA on a genomic scale in E. coli in a wide range of genetic backgrounds. Some results are expected. During log phase growth, RecA and SSB assembly profiles coincide globally, concentrated on the lagging strand and enhanced after UV irradiation. Unexpected results also abound. Near the terminus, RecA binding is favored over SSB, binding patterns change in the absence of RecG, and the absence of XerD results in massive RecA assembly. RecA may substitute for the absence of XerCD to resolve chromosome dimers. A RecA loading pathway may exist that is independent of RecBCD and RecFOR. Two prominent and focused peaks of RecA binding revealed a pair of 222 bp and GC-rich repeats, equidistant from dif and flanking the Ter domain. The repeats, here named RRS for replication risk sequence, trigger a genomically programmed generation of post-replication gaps that may play a special role in relieving topological stress during replication termination and chromosome segregation. As demonstrated here, ssGap-seq provides a new window on previously inaccessible aspects of ssDNA metabolism.

DNA Sequence Specificity Reveals a Role of the HLTF HIRAN Domain in the Recognition of Trinucleotide Repeats.

DNA damage tolerance (DDT) pathways enable cells to cope with a variety of replication blocks that threaten their ability to complete DNA replication. Helicase-like transcription factor (HLTF) plays a central role in the error-free DDT pathway, template switching (TS), by serving as a ubiquitin ligase to polyubiquitinate the DNA sliding clamp PCNA, which promotes TS initiation. HLTF also serves as an ATP-dependent DNA translocase facilitating replication fork remodeling. The HIP116, Rad5p N-terminal (HIRAN) domain of HLTF specifically recognizes the unmodified 3'-end of single-stranded DNA (ssDNA) at stalled replication forks to promote fork regression. Several crystal structures of the HIRAN domain in complex with ssDNA have been reported; however, optimal ssDNA sequences for high-affinity binding with the domain have not been described. Here we elucidated DNA sequence preferences of HLTF HIRAN through systematic studies of its binding to ssDNA substrates using fluorescence polarization assays and a computational analysis of the ssDNA:HIRAN interaction. These studies reveal that the HLTF HIRAN domain preferentially recognizes a (T/C)TG sequence at the 3'-hydroxyl ssDNA end, which occurs in the CTG trinucleotide repeat (TNR) regions that are susceptible to expansion and deletion mutations identified in neuromuscular and neurodegenerative disorders. These findings support a role for HLTF in maintaining the stability of difficult to replicate TNR microsatellite regions.

Chromosomal synapsis defects can trigger oocyte apoptosis without elevating numbers of persistent DNA breaks above wild-type levels.

Generation of haploid gametes depends on a modified version of homologous recombination in meiosis. Meiotic recombination is initiated by single-stranded DNA (ssDNA) ends originating from programmed DNA double-stranded breaks (DSBs) that are generated by the topoisomerase-related SPO11 enzyme. Meiotic recombination involves chromosomal synapsis, which enhances recombination-mediated DSB repair, and thus, crucially contributes to genome maintenance in meiocytes. Synapsis defects induce oocyte apoptosis ostensibly due to unrepaired DSBs that persist in asynaptic chromosomes. In mice, SPO11-deficient oocytes feature asynapsis, apoptosis and, surprisingly, numerous foci of the ssDNA-binding recombinase RAD51, indicative of DSBs of unknown origin. Hence, asynapsis is suggested to trigger apoptosis due to inefficient DSB repair even in mutants that lack programmed DSBs. By directly detecting ssDNAs, we discovered that RAD51 is an unreliable marker for DSBs in oocytes. Further, SPO11-deficient oocytes have fewer persistent ssDNAs than wild-type oocytes. These observations suggest that oocyte quality is safeguarded in mammals by a synapsis surveillance mechanism that can operate without persistent ssDNAs.

Increasing the λ-Red mediated gene deletion efficiency in Escherichia coli using methyl phosphotriester-modified DNA

BackgroundPhage λ-Red recombineering is a powerful genetic tool to edit the bacterial genome. With the demand of the multiplex genome editing, the efficiency of recombineering is worthy to be further improved. MethodsThe methyl phosphotriester (MPTE)-modified DNA (MPTEDNA) was used as a supplemental molecule during the electroporation of linear DNA, where the MPTEDNA was single-stranded, 69-nt long, had 5 methylation sites on its 5′-end region, and had a sequence complementary to the dsDNA for recombineering. Significant findingsThis study is the first to demonstrate that MPTEDNAs enhance the transformation efficiency (TE) for ldhA deletion and for frdABCD deletion by 6- and 12-fold, respectively, with a low total dsDNA loading of 40–70 ng. It is suggested that MPTEDNA acts a protective agent and forms the stable ssDNA-MPTEDNA duplex, where the 3′end of ssDNA is critical in both ssDNA-annealing model and recA-dependent double-strand invasion recombination model. When the duplex reaches the target gene site, the ssDNA intermediate is interchanged and annealed due to a higher melting temperature (Tm) between the ssDNA and the target gene site than that between ssDNA and MPTEDNA. The DNA duplex formation with the DNA protective agent may apply to other genomic or biomedical studies.

In vivofluorescent TUNEL detection of single stranded DNA gaps and breaks induced bydnaBhelicase mutants inEscherichia coli.

The genome of prokaryotes can be damaged by a variety of endogenous and exogenous factors, including reactive oxygen species, UV exposure, and antibiotics. To better understand these repair processes and the impact they may have on DNA replication, normal genome maintenance processes can be perturbed by removing or editing associated genes and monitoring DNA repair outcomes. In particular, the replisome activities of DNA unwinding by the helicase and DNA synthesis by the polymerase must be tightly coupled to prevent any appreciable single strand DNA (ssDNA) from accumulating and amplifying genomic stress. If decoupled, vulnerable ssDNA would persist, likely leading to double strand breaks (DSBs) or requiring replication restart mechanisms downstream of a stall. In either case, free 3'-OH strands would exist, resulting from ssDNA gaps in the leading strand or complete DSBs. Terminal deoxyribonucleotide transferase (TdT)-mediated dUTP nick end labeling (TUNEL) can enzymatically label ssDNA ends with bromo-deoxy uridine triphosphate (BrdU) to detect free 3'-OH DNA ends in the E. coli genome. Labeled DNA ends can be detected and quantified using fluorescence microscopy or flow cytometry. This methodology is useful in applications where in situ investigation of DNA damage and repair are of interest, including effects from enzyme mutations or deletions and exposure to various environmental conditions.

RNA-DNA hybrids regulate meiotic recombination.

RNA-DNA hybrids are often associated with genome instability and also function as a cellular regulator in many biological processes. In this study, we show that accumulated RNA-DNA hybrids cause multiple defects in budding yeast meiosis, including decreased sporulation efficiency and spore viability. Further analysis shows that these RNA-DNA hybrid foci colocalize with RPA/Rad51 foci on chromosomes. The efficient formation of RNA-DNA hybrid foci depends on Rad52 and ssDNA ends of meiotic DNA double-strand breaks (DSBs), and their number is correlated with DSB frequency. Interestingly, RNA-DNA hybrid foci and recombination foci show similar dynamics. The excessive accumulation of RNA-DNA hybrids around DSBs competes with Rad51/Dmc1, impairs homolog bias, and decreases crossover and noncrossover recombination. Furthermore, precocious removal of RNA-DNA hybrids by RNase H1 overexpression also impairs meiotic recombination similarly. Taken together, our results demonstrate that RNA-DNA hybrids form at ssDNA ends of DSBs to actively regulate meiotic recombination.

Target-receptive structural switching of ssDNA as selective and sensitive biosensor for subsequent detection of toxic Pb2+ and organophosphorus pesticide

A structural switching in Single-stranded DNA (ssDNA) fluorescence biosensor for quick turn-on/off detection of Pb2+ ions and pesticide was reported. The design strategy of Hex-labelled ssDNA consists of two types of aptamer probe, G-rich base pair sequence forms G-quadruplex confirmation with Pb2+ ions. While other part of base pair sequence exhibits affinity to fold isocarbophos pesticide. MoS2 nanosheets were identified as quick quencher of Hex fluorescence intensity via Vander-Waals interaction and its significance was compared with other nanomaterials. This sensing mechanism proposes a specific affinity of GA-rich ssDNA with Pb2+ to form G-quadruplex via G-Pb2+-G sequences. Consequently, ssDNA relived from MoS2 nanosheets to restore the fluorescence intensity (turn-on). Subsequent addition of pesticide shows stronger affinity towards unfolded aptamer probe to form a random coil like structure. This causes Hex-labelled 5′ end closer to the G-quadruplex connected at the 3’ end of ssDNA resulting in a remarkable fluorescence quenching (turn-off) owing to PET process. Moreover, the sensing probe (Hex-labelled GA-rich ssDNA) was recycled by introducing acetylcholinesterase enzyme and thiocoline into the reaction mixture. The detection limits of Pb2+ and isocarbophos pesticide was estimated to be 0.6 nM and 0.018 μg/L respectively. Moreover, this study reveals a high sensitivity and selectivity towards target molecules in environmental samples.

Label-Free Imaging of Flap Endonuclease 1 in Living Cells by Assembling Original and Multifunctional Nanoprobe.

Flap endonuclease 1 (FEN1) becomes a potential tumor marker since it is closely related to cancer occurrence and development. Here, a poly dA20-mediated nanoprobe (AuNPs-poly dA20-poly dT20) was designed for FEN1 detection. Poly dA20 segment at the 3'- end of ssDNA adsorbed on AuNPs due to its strong affinity interaction with Au (stronger than Au-S bond), while the poly dT20 segment at the 5'- end overhangs. This nanoprobe not only worked as effective fluorescence quencher but also as the original nanosubstrate of FEN1. OliGreen adsorbed on poly dT20 emits strong green fluorescence because of its high sensitivity and selectivity toward thymine. However, it is quenched on the nanoprobe. In the presence of FEN1, it recognizes the overhanging poly dT20 segment and cleaves it efficiently, turning on the fluorescence of OliGreen. This indicates that the assembled nanoprobe is an effective artificial substrate to FEN1, although it is completely different from previously reported substrates that are all composed of dsDNA with a flap strand. This proposed nanoprobe was used to detect FEN1 not only in vitro but also in vivo. The method was simple, which avoided complex labeling procedures. It had a wide linear range from 0.05 U to 2 U, with the lowest detection limit of 0.007 U. Confocal imaging can distinguish cancer cells from normal cells, demonstrating its potential in clinical diagnostic and therapeutic monitoring.

Probing Conformational Polymorphism of DNA Assemblies with Nanopores.

Single-stranded DNA (ssDNA) can be designed to assemble into duplexes and other high-order structures through Watson-Crick hydrogen bonds. Incorporation of unnatural nucleobases or binding with small molecules can also introduce new interactions that give rise to novel DNA assemblies. However, the methods for determining the conformational properties of DNA assemblies are still very limited. Here we develop a new strategy for probing conformational polymorphism of different DNA assemblies. By installing poly(dC)30 tails to the ends of individual ssDNA that assemble into duplex, triplex, or other complex structures, we are able to observe different current blockade patterns corresponding to specific DNA nanostructures when the DNA assemblies are lodged inside α-hemolysin vestibule. We can also monitor the disassembly of the DNA nanostructures in solution. This method complements the existing traditional technologies such as circular dichroism spectroscopy, fluorescence labeling, and NMR spectroscopy, and shows distinct advantages of high accuracy and general applicability.

TEX264 coordinates p97- and SPRTN-mediated resolution of topoisomerase 1-DNA adducts

Eukaryotic topoisomerase 1 (TOP1) regulates DNA topology to ensure efficient DNA replication and transcription. TOP1 is also a major driver of endogenous genome instability, particularly when its catalytic intermediate—a covalent TOP1-DNA adduct known as a TOP1 cleavage complex (TOP1cc)—is stabilised. TOP1ccs are highly cytotoxic and a failure to resolve them underlies the pathology of neurological disorders but is also exploited in cancer therapy where TOP1ccs are the target of widely used frontline anti-cancer drugs. A critical enzyme for TOP1cc resolution is the tyrosyl-DNA phosphodiesterase (TDP1), which hydrolyses the bond that links a tyrosine in the active site of TOP1 to a 3’ phosphate group on a single-stranded (ss)DNA break. However, TDP1 can only process small peptide fragments from ssDNA ends, raising the question of how the ~90 kDa TOP1 protein is processed upstream of TDP1. Here we find that TEX264 fulfils this role by forming a complex with the p97 ATPase and the SPRTN metalloprotease. We show that TEX264 recognises both unmodified and SUMO1-modifed TOP1 and initiates TOP1cc repair by recruiting p97 and SPRTN. TEX264 localises to the nuclear periphery, associates with DNA replication forks, and counteracts TOP1ccs during DNA replication. Altogether, our study elucidates the existence of a specialised repair complex required for upstream proteolysis of TOP1ccs and their subsequent resolution.

Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.

Whole-genome bisulfite sequencing (WGBS) is the current gold standard of methylome analysis. Post-bisulfite adaptor tagging (PBAT) is an increasingly popular WGBS protocol because of high sensitivity and low bias. PBAT originally relied on two rounds of random priming for adaptor-tagging of single-stranded DNA (ssDNA) to attain high efficiency but at a cost of library insert length. To overcome this limitation, we developed terminal deoxyribonucleotidyl transferase (TdT)-assisted adenylate connector-mediated ssDNA (TACS) ligation as an alternative to random priming. In this method, TdT attaches adenylates to the 3′-end of input ssDNA, which are then utilized by RNA ligase as an efficient connector to the ssDNA adaptor. A protocol that uses TACS ligation instead of the second random priming step substantially increased the lengths of PBAT library fragments. Moreover, we devised a dual-library strategy that splits the input DNA to prepare two libraries with reciprocal adaptor polarity, combining them prior to sequencing. This strategy ensured an ideal base–color balance to eliminate the need for DNA spike-in for color compensation, further improving the throughput and quality of WGBS. Adopting the above strategies to the HiSeq X Ten and NovaSeq 6000 platforms, we established a cost-effective, high-quality WGBS, which should accelerate various methylome analyses.

XPG-related nucleases are hierarchically recruited for double-stranded rDNA break resection

dsDNA breaks (DSBs) are resected in a 5'→3' direction, generating single-stranded DNA (ssDNA). This promotes DNA repair by homologous recombination and also assembly of signaling complexes that activate the DNA damage checkpoint effector kinase Chk1. In fission yeast (Schizosaccharomyces pombe), genetic screens have previously uncovered a family of three xeroderma pigmentosum G (XPG)-related nucleases (XRNs), known as Ast1, Exo1, and Rad2. Collectively, these XRNs are recruited to a euchromatic DSB and are required for ssDNA production and end resection across the genome. Here, we studied why there are three related but distinct XRN enzymes that are all conserved across a range of species, including humans, whereas all other DSB response proteins are present as single species. Using S. pombe as a model, ChIP and DSB resection analysis assays, and highly efficient I-PpoI-induced DSBs in the 28S rDNA gene, we observed a hierarchy of recruitment for each XRN, with a progressive compensatory recruitment of the other XRNs as the responding enzymes are deleted. Importantly, we found that this hierarchy reflects the requirement for different XRNs to effect efficient DSB resection in the rDNA, demonstrating that the presence of three XRN enzymes is not a simple division of labor. Furthermore, we uncovered a specificity of XRN function with regard to the direction of transcription. We conclude that the DSB-resection machinery is complex, is nonuniform across the genome, and has built-in fail-safe mechanisms, features that are in keeping with the highly pathological nature of DSB lesions.

A label-free hairpin aptamer probe for colorimetric detection of adenosine triphosphate based on the anti-aggregation of gold nanoparticles.

A facile and rapid colorimetric approach was described for selective and sensitive determination of adenosine triphosphate (ATP) based on a hairpin aptamer probe and the anti-aggregation of AuNPs. Poly(diallyldimethylammonium chloride) (PDDA) can induce the aggregation of AuNPs due to the electrostatic interaction causing a red to blue color change. Upon the addition of ATP, aptamer-based hairpin probe is opened and releases flexible ssDNA ends. The released flexible ssDNA ends can interact with PDDA and prevent PDDA-induced AuNPs aggregation. Thus, a visible color change from blue to red and a decrease in the absorption ratio (A610/A520) are observed. Under the optimal conditions, the hairpin aptamer-based colorimetric assay exhibits high sensibility and selectivity for the detection of ATP with a detection limit of 1.7nM. Moreover, this assay is successfully used in the rapid determination of ATP in spiked human serum samples with good recoveries in the range of 102.88 to 104.07%.

Measuring the Conformation and Persistence Length of Single-Stranded DNA Using a DNA Origami Structure.

Measuring the mechanical properties of single-stranded DNA (ssDNA) is a challenge that has been addressed by different methods lately. The short persistence length, fragile structure, and the appearance of stem loops complicate the measurement, and this leads to a large variability in the measured values. Here we describe an innovative method based on DNA origami for studying the biophysical properties of ssDNA. By synthesizing a DNA origami structure that consists of two rigid rods with an ssDNA segment between them, we developed a method to characterize the effective persistence length of a random-sequence ssDNA while allowing the formation of stem loops. We imaged the structure with an atomic force microscope (AFM); the rigid rods provide a means for the exact identification of the ssDNA ends. This leads to an accurate determination of the end-to-end distance of each ssDNA segment, and by fitting the measured distribution to the ideal chain polymer model we measured an effective persistence length of 1.98 ± 0.72 nm. This method enables one to measure short or long strands of ssDNA, and it can cope with the formation of stem loops that are often formed along ssDNA. We envision that this method can be used for measuring stem loops for determining the effect of repetitive nucleotide sequences and environmental conditions on the mechanical properties of ssDNA and the effect of interacting proteins with ssDNA. We further noted that the method can be extended to nanoprobes for measuring the interactions of specific DNA sequences, because the DNA origami rods (or similar structures) can hold multiple fluorescent probes that can be easily detected.

Triazole linking for preparation of a next-generation sequencing library from single-stranded DNA.

Next-generation sequencing of single-stranded DNA (ssDNA) is attracting increased attention from a wide variety of research fields. Accordingly, various methods are actively being tested for the efficient adaptor-tagging of ssDNA. We conceived a novel chemo-enzymatic method termed terminal deoxynucleotidyl transferase (TdT)-assisted, copper-catalyzed azide-alkyne cycloaddition (CuAAC)-mediated ssDNA ligation (TCS ligation). In this method, TdT is used to incorporate a single 3′-azide-modified dideoxyribonucleotide onto the 3′-end of target ssDNA, followed by CuAAC-mediated click ligation of the azide-incorporated 3′-end to a 5′-ethynylated synthetic adaptor. This report presents the first proof-of-principle application of TCS ligation with its use in the preparation of a next-generation sequencing library.

Influence of amine and thiol modifications at the 3′ ends of single stranded DNA molecules on their adsorption on gold surface and the efficiency of their hybridization

Adsorption of molecules of DNA (deoxyribonucleic acid) or modified DNA on gold surfaces is often the first step in construction of many various biosensors, including biosensors for detection of DNA with a particular sequence. In this work we study the influence of amine and thiol modifications at the 3′ ends of single stranded DNA (ssDNA) molecules on their adsorption on the surface of gold substrates and on the efficiency of hybridization of immobilized DNA with the complementary single stranded DNA. The characterization of formed layers has been carried out using infrared spectroscopy and atomic force microscopy. As model single stranded DNA we used DNA containing 20 adenine bases, whereas the complementary DNA contained 20 thymine bases. We found that the bands in polarization modulation-infrared reflection-adsorption spectroscopy (PM-IRRAS) spectra of layers formed from thiol-modified DNA are significantly narrower and sharper, indicating their higher regularity in the orientation of DNA on gold surface when using thiol linker. Also, hybridization of the layer of thiol-modified DNA containing 20 adenine bases with the respective DNA containing thymine bases leads to formation of much more organized structures than in the case of unmodified DNA or DNA with the amine linker. We conclude that the thiol-modified ssDNA is more promising for the preparation of biosensors, in comparison with the amine-modified or unmodified ssDNA. We have also found that the above-mentioned modifications at the 3′ end of ssDNA significantly influence the IR spectrum (and hence the structure) of polycrystalline films formed from such compounds, even though adsorbed fragments contain less than 5% of the DNA chain. This effect should be taken into account when comparing IR spectra of various polycrystalline films formed from modified and unmodified DNA.

The Sulfolobus solfataricus RecQ-like DNA helicase Hel112 inhibits the NurA/HerA complex exonuclease activity.

ATPase/Helicases and nucleases play important roles in DNA end-resection, a critical step during homologous recombination repair in all organisms. In hyperthermophilic archaea the exo-endonuclease NurA and the ATPase HerA cooperate with the highly conserved Mre11-Rad50 complex in 3' single-stranded DNA (ssDNA) end processing to coordinate repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA complex. In this study we demonstrate that the NurA exonuclease activity is inhibited by the Sulfolobus solfataricus RecQ-like Hel112 helicase. Inhibition occurs both in the presence and in the absence of HerA, but is much stronger when NurA is in complex with HerA. In contrast, the endonuclease activity of NurA is not affected by the presence of Hel112. Taken together these results suggest that the functional interaction between NurA/HerA and Hel112 is important for DNA end-resection in archaeal homologous recombination.

Structure of mycobacterial 3'-to-5' RNA:DNA helicase Lhr bound to a ssDNA tracking strand highlights distinctive features of a novel family of bacterial helicases.

Mycobacterial Lhr is a DNA damage-inducible superfamily 2 helicase that uses adenosine triphosphate (ATP) hydrolysis to drive unidirectional 3′-to-5′ translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes en route. ATPase, translocase and helicase activities are encompassed within the N-terminal 856-amino acid segment. The crystal structure of Lhr-(1–856) in complex with AMPPNP•Mg2+ and ssDNA defines a new helicase family. The enzyme comprises two N-terminal RecA-like modules, a winged helix (WH) domain and a unique C-terminal domain. The 3′ ssDNA end binds in a crescent-shaped groove at the interface between the first RecA domain and the WH domain and tracks 5′ into a groove between the second RecA and C domains. A kissing interaction between the second RecA and C domains forms an aperture that demarcates a putative junction between the loading strand tail and the duplex, with the first duplex nucleoside bookended by stacking on Trp597. Intercalation of Ile528 between nucleosides of the loading strand creates another bookend. Coupling of ATP hydrolysis to RNA:DNA unwinding is dependent on Trp597 and Ile528, and on Thr145 and Arg279 that contact phosphates of the loading strand. The structural and functional data suggest a ratchet mechanism of translocation and unwinding coupled to ATP-driven domain movements.

Electrochemical DNA biosensor based on gold nanoparticles and partially reduced graphene oxide modified electrode for the detection of Listeria monocytogenes hly gene sequence

In this study an electrochemical DNA biosensor with gold nanoparticles (AuNPs) and partially reduced graphene oxide (p-RGO) modified electrode was constructed to detect Listeria monocytogenes hly gene sequence. AuNPs were electrodeposited on the surface of carbon ionic liquid electrode (CILE) and then p-RGO was further deposited at controlled electroreduction conditions. On the p-RGO surface unreduced oxygenal groups were present and could covalently interact with the amine group at the 5′-end of probe ssDNA through carbodiimide linkage, and the resulted ssDNA/p-RGO/AuNPs/CILE could be used to hybridize with the target ssDNA sequence. Differential pulse voltammetry was applied to monitor the DNA hybridization with methylene blue as electrochemical indicator. Under the optimal conditions, the electrochemical biosensor could be applied to the detection of target DNA sequence in the concentration range from 1.0×10−13–1.0×10−6mol/L with the detection limit of 3.17×10−14mol/L (3S0/S). The sensor exhibited good stability and selectivity to one or three-base mismatched ssDNA sequences. PCR sample of Listeria monocytogenes hly gene sequence was successfully detected, indicating the real application of this biosensor.