Rolling circle amplification is a rapid, sensitive and isothermal single-stranded DNA amplification technique that can be used with staining or probes to amplify the detection signal. This technology has been widely used in biological detection and other aspects. The present paper introduces how to design rolling circle amplification, summarize its application in the detection of pathogens, nucleic acid tumor markers, proteins, biological small biomolecules, and viruses in recent years and prospects for future development.
DNA, Single-Stranded ; Nucleic Acid Amplification Techniques

BACKGROUND: Skin hydration is a common problem both in elderly and young people as dry skin may cause irritation, dermatological disorders, and wrinkles. While both genetic and environmental factors seem to influence skin hydration, thorough genetic studies on skin hydration have not yet been conducted. OBJECTIVE: We used a genome-wide association study (GWAS) to explore the genetic elements underlying skin hydration by regulating epidermal differentiation and skin barrier function. METHODS: A GWAS was conducted to investigate the genetic factors influencing skin hydration in 100 Korean females along with molecular studies of genes in human epidermal keratinocytes for functional study in vitro. RESULTS: Among several single nucleotide polymorphisms identified in GWAS, we focused on Single Stranded DNA Binding Protein 3 (SSBP3) which is associated with DNA replication and DNA damage repair. To better understand the role of SSBP3 in skin cells, we introduced a calcium-induced differentiation keratinocyte culture system model and found that SSBP3 was upregulated in keratinocytes in a differentiation dependent manner. When SSBP3 was overexpressed using a recombinant adenovirus, the expression of differentiation-related genes such as loricrin and involucrin was markedly increased. CONCLUSION: Taken together, our results suggest that genetic variants in the intronic region of SSBP3 could be determinants in skin hydration of Korean females. SSBP3 represents a new candidate gene to evaluate the molecular basis of the hydration ability in individuals.
Adenoviridae ; Aged ; Cell Differentiation ; DNA Damage ; DNA Replication ; DNA, Single-Stranded* ; DNA-Binding Proteins* ; Female ; Genome-Wide Association Study ; Humans ; In Vitro Techniques ; Introns ; Keratinocytes ; Polymorphism, Single Nucleotide ; Skin*

A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and applied it to scan National Center for Biotechnology Information (NCBI) RefSeq bacterial genome sequences. Among 16,844 bacterial sequences possessing a retron-type RT domain, we identified 48 unique types of msDNA. Currently, the biological role of msDNA is not well understood. Our work will be a useful tool in studying the distribution, evolution, and physiological role of msDNA.
Biotechnology ; Chimera ; DNA ; DNA, Single-Stranded* ; Genome, Bacterial* ; Retroelements ; Reverse Transcription ; RNA ; RNA-Directed DNA Polymerase

Although some mutations are beneficial and are the driving force behind evolution, it is important to maintain DNA integrity and stability because it contains genetic information. However, in the oxygen-rich environment we live in, the DNA molecule is under constant threat from endogenous or exogenous insults. DNA damage could trigger the DNA damage response (DDR), which involves DNA repair, the regulation of cell cycle checkpoints, and the induction of programmed cell death or senescence. Dysregulation of these physiological responses to DNA damage causes developmental defects, neurological defects, premature aging, infertility, immune system defects, and tumors in humans. Some human syndromes are characterized by unique neurological phenotypes including microcephaly, mental retardation, ataxia, neurodegeneration, and neuropathy, suggesting a direct link between genomic instability resulting from defective DDR and neuropathology. In this review, rare human genetic disorders related to abnormal DDR and damage repair with neural defects will be discussed.
Aging ; Aging, Premature ; Ataxia ; Cell Cycle Checkpoints ; Cell Death ; Central Nervous System Diseases ; DNA Breaks, Double-Stranded ; DNA Breaks, Single-Stranded ; DNA Damage* ; DNA Repair ; DNA* ; Genomic Instability ; Humans* ; Immune System ; Infertility ; Intellectual Disability ; Microcephaly ; Neuropathology ; Phenotype

OBJECTIVETo develop a novel colorimetric method for detecting the tumor biomarker vascular endothelial growth factor (VEGF) based on aptamer and magnetic beads.

METHODSThe capture aptamer was hybridized to urease functionalized single-stranded DNA (ssDNA) and immobilize on the surface of magnetic beads by specific biotin-avidin binding. In the presence of VEGF, aptamers bound to VEGF to form a specific stem-loop structure to release the urease functionalized ssDNA. After separation, the supernatant was transferred to a tube and urea and phenol red were added. Urease hydrolyzed urea to produce ammonia to cause an increase of the pH value and a color change of phenol red. The results were inspected with either the naked eyes or by a UV spectrophotometer.

RESULTSUnder optimized conditions, the detection system showed a good linear relationship for VEGF detection in the range of 0.1 to 10 pmol/L with a detection limit as low as 0.06 pmol/L. The results of VEGF detection in the serum of patients with lung cancer were consistent with those using an ELISA Kit. The results of examination of 10 serum samples with this aptamer-based method and ELISA kit showed that the accuracy of this method was 90%.

CONCLUSIONThis aptamer-based system provides an simple and convenient method for VEGF detection with a high sensitivity and selectivity.

Aptamers, Nucleotide ; Biomarkers, Tumor ; Colorimetry ; DNA, Single-Stranded ; Humans ; Lung Neoplasms ; Nucleic Acid Hybridization ; Vascular Endothelial Growth Factor A ; analysis

No abstract available.
Bone Marrow/metabolism/pathology ; DNA Mutational Analysis ; Gene Rearrangement, T-Lymphocyte ; Humans ; Immunophenotyping ; Infant ; Lymphohistiocytosis, Hemophagocytic/*diagnosis ; Male ; Membrane Proteins/chemistry/genetics ; Polymorphism, Single-Stranded Conformational ; Republic of Korea ; T-Lymphocytes/immunology/*metabolism

AAV-ITR gene expression mini vector is a double-strand or single-strand DNA that only contains inverted terminal repeats of adeno-associated virus, cis-elements and gene of interest and does not contain any other foreign DNA sequences. We prepared Bac-ITR-EGFP and Bac-inrep. Spodoptera frugiperda cells were infected with Bac-ITR-EGFP (P3) and Bac-inrep (P3). Up to 100 μg of AAV-ITR-EGFP gene expression mini vectors were extracted from 2 x 10(7) cells of Sf9 72 h after infection. The gel electrophoresis analysis shows that most forms of AAV-ITR-EGFP gene expression mini vector were monomer and dimer. The mini vector expression efficacy was examined in vitro with HEK 293T cells. The EGFP expression was observed at 24 h after transfection, and the positive ratio reached 65% at 48 h after transfection.
Animals ; Baculoviridae ; DNA, Single-Stranded ; Dependovirus ; Gene Expression ; Genetic Vectors ; HEK293 Cells ; Humans ; Sf9 Cells ; Terminal Repeat Sequences ; Transfection

OBJECTIVETo observe the characteristics of sperm single-stranded DNA breaks (SSB) and double-stranded DNA breaks (DSB) in infertile men, explore the association of DSB with male infertility, and provide a new observation index and idea for the diagnosis and treatment of the disease.

METHODSThis study involved 60 infertile men (infertility group) and 30 normal healthy males with infertile wives (control group). We comparatively analyzed the seminal parameters of the two groups, determined sperm concentration and viability using the computer aided sperm analysis system, measured the sperm survival rate by hypoosmotic swelling (HOS) test, examined sperm morphology by Diff-Quick staining, and detected sperm DNA damage by two-tail comet assay.

RESULTSNine two-tail comet models were established for detecting sperm DNA integrity. Comparisons between the fertility and control groups showed that the sperm DNA fragmentation index (DFI) was (33.8 ± 13.1) vs (16.3 ± 7.9)% (P < 0.01), the SSB-DFI was (19.2 ± 11.4) vs (14.9 ± 7.6)% (P > 0.05), the SSB-DFI/DFI was (56.8 ± 32.4) vs (91.4 ± 27.8)% (P < 0.01), the DSB-DFI was (23.9 +13.4) vs (6.1 ± 2.7)% (P < 0.01), and the DSB-DFI/DFI was (70.8 ± 19.5) vs (37.4 ± 11.3)% (P < 0.01). The optimal cut-off value of DSB-DFI/DFI in the diagnosis of male infertility was 39.5%, with the AUG, sensitivity, and specificity of 0.969, 98.3%, and 90%; that of DSB-DFI was 15.85%, with the AUC, sensitivity, and specificity of 0.912, 86.7%, and 80%; and that of DFI was 18.65%; with the AUC, sensitivity, and specificity of 0.861, 90%, 70%, respectively. In the infertile men, neither SSB-DFI nor SSB-DFI/DFI exhibited any correlation with semen parameters (P > 0.05); DFI was correlated negatively with the percentage of progressively motile sperm, sperm survival rate, and the percentage of morphologically normal sperm (P < 0.05 or P < 0.01), but not correlated with sperm concentration (P > 0.05); both DSB-DFI and DSB-DFI/DFI showed a negative correlation with sperm concentration, sperm survival rate, and the percentages of progressively motile sperm and morphologically normal sperm (P < 0.05 or P < 0.01).

CONCLUSIONDouble-stranded, rather than single-stranded DNA breaks, may be a factor inducing male infertility. The type of sperm DNA strand damage is of much reference value for the assessment of male fertility.

Case-Control Studies ; Comet Assay ; DNA Breaks, Double-Stranded ; DNA Breaks, Single-Stranded ; DNA Fragmentation ; Fertility ; Humans ; Infertility, Male ; diagnosis ; genetics ; Male ; Semen Analysis ; Sensitivity and Specificity ; Sperm Count ; Spermatozoa ; Staining and Labeling

OBJECTIVETo investigate single-molecule detection and characterization of DNA replication.

METHODSSingle-stranded DNA (ssDNA) as the template of DNA replication was attached to DNA origami by a hybridization reaction based on the complementary base-pairing principle. DNA replication catalyzed by E.coli DNA polymerase I Klenow Fragment (KF) was detected using atomic force microscopy (AFM). The height variations between the ssDNA and the double-stranded DNA (dsDNA), the distribution of KF during DNA replication and biotin-streptavidin (BA) complexes on the DNA strand after replication were detected. Agarose gel electrophoresis was employed to analyze the changes in the DNA after replication.

RESULTSThe designed ssDNA could be anchored on the target positions of over 50% of the DNA origami. The KF was capable of binding to the ssDNA fixed on DNA origami and performing its catalytic activities, and was finally dissociated from the DNA after replication. The height of DNA strand increased by about 0.7 nm after replication. The addition of streptavidin also resulted in an DNA height increase to about 4.9 nm due to the formation of BA complexes on the biotinylated dsDNA. The resulting dsDNA and BA complex were subsequently confirmed by agarose gel electrophoresis.

CONCLUSIONSThe combination of AFM and DNA origami allows detection and characterization of DNA replication at the single molecule level, and this approach provides better insights into the mechanism of DNA polymerase and the factors affecting DNA replication.

Biotinylation ; DNA ; chemistry ; DNA Replication ; DNA, Single-Stranded ; chemistry ; DNA-Directed DNA Polymerase ; Electrophoresis, Agar Gel ; Microscopy, Atomic Force ; Nucleic Acid Hybridization ; Streptavidin

BACKGROUND/OBJECTIVE: Myocardial cell death due to occlusion of the coronary arteries leads to myocardial infarction, a subset of coronary heart disease (CHD). Dietary fiber is known to be associated with a reduced risk of CHD, the underlying mechanisms of which were suggested to delay the onset of occlusion by ameliorating risk factors. In this study, we tested a hypothesis that a beneficial role of dietary fiber could arise from protection of myocardial cells against ischemic injury, manifested after occlusion of the arteries. MATERIALS/METHODS: Three days after rats were fed apple pectin (AP) (with 10, 40, 100, and 400 mg/kg/day), myocardial ischemic injury was induced by 30 min-ligation of the left anterior descending coronary artery, followed by 3 hr-reperfusion. The area at risk and infarct area were evaluated using Evans blue dye and 2,3,5-triphenyltetrazolium chloride (TTC) staining, respectively. DNA nicks reflecting the extent of myocardial apoptosis were assessed by TUNEL assay. Levels of cleaved caspase-3, Bcl-2, and Bax were assessed by immunohistochemistry. RESULTS: Supplementation of AP (with 100 and 400 mg/kg/day) resulted in significantly attenuated infarct size (IS) (ratio of infarct area to area at risk) by 21.9 and 22.4%, respectively, in the AP-treated group, compared with that in the control group. This attenuation in IS showed correlation with improvement in biomarkers involved in the apoptotic cascades: reduction of apoptotic cells, inhibition of conversion of procaspase-3 to caspase-3, and increase of Bcl-2/Bax ratio, a determinant of cell fate. CONCLUSIONS: The findings indicate that supplementation of AP results in amelioration of myocardial infarction by inhibition of apoptosis. Thus, the current study suggests that intake of dietary fiber reduces the risk of CHD, not only by blocking steps leading to occlusion, but also by protecting against ischemic injury caused by occlusion of the arteries.
Animals ; Apoptosis* ; Arteries ; Biomarkers ; Caspase 3 ; Cell Death ; Coronary Disease ; Coronary Vessels ; Dietary Fiber* ; DNA Breaks, Single-Stranded ; Evans Blue ; Immunohistochemistry ; In Situ Nick-End Labeling ; Ischemia ; Models, Animal* ; Myocardial Infarction ; Rats ; Risk Factors