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Journal articles on the topic 'Ss(ds-)-DNA'

Author: Grafiati

Published: 11 March 2023

Last updated: 31 July 2025

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1

Chandran, Harish, Nikhil Gopalkrishnan, Bernard Yurke, and John Reif. "Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions." Journal of The Royal Society Interface 9, no. 72 (2012): 1637–53. http://dx.doi.org/10.1098/rsif.2011.0819.

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Can a wide range of complex biochemical behaviour arise from repeated applications of a highly reduced class of interactions? In particular, can the range of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands of DNA as the only component molecules. Various enzymatic manipulations of these mDNA molecules are simulated via toehold-mediated DNA strand displacement reactions. We provide a formal model to describe the required properties and op

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2

Liu, H., M. I. Boulton, C. L. Thomas, D. A. M. Prior, K. J. Oparka, and J. W. Davies. "Maize Streak Virus Coat Protein Is Karyophyllic and Facilitates Nuclear Transport of Viral DNA." Molecular Plant-Microbe Interactions® 12, no. 10 (1999): 894–900. http://dx.doi.org/10.1094/mpmi.1999.12.10.894.

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Transport of maize streak virus (MSV) DNA into the nucleus of host cells is essential for virus replication and the presence of virus particles in the nuclei of infected cells implies that coat protein (CP) must enter the nucleus. To see if CP is imported into the nucleus in the absence of other viral gene products, the MSV CP gene was expressed in insect cells with a baculovirus vector system, and also in tobacco protoplasts with a cauliflower mosaic virus (CaMV) 35S promoter-driven transient gene expression vector. Immunofluorescent staining showed that the CP accumulated in the nuclei of bo

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3

De, Pallabi, Mandy M. Peak, and Karla K. Rodgers. "DNA Cleavage Activity of the V(D)J Recombination Protein RAG1 Is Autoregulated." Molecular and Cellular Biology 24, no. 15 (2004): 6850–60. http://dx.doi.org/10.1128/mcb.24.15.6850-6860.2004.

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ABSTRACT RAG1 and RAG2 catalyze the first DNA cleavage steps in V(D)J recombination. We demonstrate that the isolated central domain of RAG1 has inherent single-stranded (ss) DNA cleavage activity, which does not require, but is enhanced by, RAG2. The central domain, therefore, contains the active-site residues necessary to perform hydrolysis of the DNA phosphodiester backbone. Furthermore, the catalytic activity of this domain on ss DNA is abolished by addition of the C-terminal domain of RAG1. The inhibitory effects of this latter domain are suppressed on substrates containing double-strande

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4

Hauck, Bernd, Wei Zhao, Katherine High, and Weidong Xiao. "Intracellular Viral Processing, Not Single-Stranded DNA Accumulation, Is Crucial for Recombinant Adeno-Associated Virus Transduction." Journal of Virology 78, no. 24 (2004): 13678–86. http://dx.doi.org/10.1128/jvi.78.24.13678-13686.2004.

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ABSTRACT Adeno-associated virus (AAV) is a unique gene transfer vector which takes approximately 4 to 6 weeks to reach its expression plateau. The mechanism for this slow-rise expression profile was proposed to be inefficient second-strand DNA synthesis from the input single-stranded (ss) DNA viral genome. In order to clarify the status of ss AAV genomes, we generated AAV vectors labeled with bromodeoxyuridine (BrdU), a nucleotide analog that can be incorporated into the AAV genome and packaged into infectious virions. Since BrdU-DNA can be detected only by an anti-BrdU antibody when DNA is in

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5

Erben, Antonija, Josipa Matić, Nikola Basarić, and Ivo Piantanida. "The Phenanthridine-modified Tyrosine Dipeptide." Croatica chemica acta 92, no. 2 (2019): 249–58. http://dx.doi.org/10.5562/cca3542.

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Dipeptide 4 containing two unnatural amino acids, a modified tyrosine and a phenanthridine derivative, was synthesized. Binding of the dipeptide to a series of polynucleotides including ct-DNA, poly A - poly U, poly (dAdT)2, poly dG - poly dC and poly (dGdC)2 was investigated by thermal denaturation experiments, fluorescence spectroscopy and circular dichroism. Thermal denaturation experiments indicated that dipeptide 4 at pH 5.0, when phenanthridine is protonated, stabilizes ds-DNA, whereas it destabilizes ds-RNA. At pH 7.0, when the phenanthridine is not protonated, effects of 4 to the polyn

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6

Bastos, M., V. Castro, G. Mrevlishvili, and J. Teixeira. "Hydration of ds-DNA and ss-DNA by Neutron Quasielastic Scattering." Biophysical Journal 86, no. 6 (2004): 3822–27. http://dx.doi.org/10.1529/biophysj.104.039586.

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7

Clausen, J., and S. A. Nielsen. "The Use of In Vitro Cultured Lymphocytes for Tracing Mutagenic Activities of Chemicals." Alternatives to Laboratory Animals 14, no. 3 (1987): 168–71. http://dx.doi.org/10.1177/026119298701400314.

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Lymphocytes from normal, non-smoking human individuals not taking drugs were isolated from the peripheral blood by means of the lymphoprep method. The cells were cultured in RPMI medium with 10% fetal calf serum and stimulated with Phytohemagglutinin. A mutagen such as 3-methylcholanthrene was added for varying periods of time. Then the subspecies of DNA, i.e. double and single stranded DNA (ds-DNA and ss-DNA), were separated by the alkaline elution technique and quantitated by fluorimetric estimation. The mutagen induced a significant rise in the level of ss-DNA, but no changes in ds-DNA coul

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8

Amundsen, S. K., A. M. Neiman, S. M. Thibodeaux, and G. R. Smith. "Genetic dissection of the biochemical activities of RecBCD enzyme." Genetics 126, no. 1 (1990): 25–40. http://dx.doi.org/10.1093/genetics/126.1.25.

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Abstract RecBCD enzyme of Escherichia coli is required for the major pathway of homologous recombination following conjugation. The enzyme has an ATP-dependent DNA unwinding activity, ATP-dependent single-stranded (ss) and double-stranded (ds) DNA exonuclease activities, and an activity that makes a ss DNA endonucleolytic cut near Chi sites. We have isolated and characterized ten mutations that reduced recombination proficiency and inactivated some, but not all, activities of RecBCD enzyme. One class of mutants had weak ds DNA exonuclease activity and lacked Chi-dependent DNA cleavage activity

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9

Kirisawa, Rikio, Rika Kato, Koichi Furusaki, and Takashi Onodera. "Universal Virucidal Activity of Calcium Bicarbonate Mesoscopic Crystals That Provides an Effective and Biosafe Disinfectant." Microorganisms 10, no. 2 (2022): 262. http://dx.doi.org/10.3390/microorganisms10020262.

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We investigated the virucidal effects in solution of a new type of disinfectant, calcium bicarbonate mesoscopic crystals, designated CAC-717, against various types of virus. CAC-717 in solution is alkaline (pH 12.4) and has a self-electromotive force that generates pulsed electrical fields. Upon application to human skin, the pH of the solution becomes 8.4. CAC-717 contains no harmful chemicals and is thus non-irritating and harmless to humans and animals. Its virucidal effects were tested against six types of animal virus: enveloped double-strand (ds)-DNA viruses, non-enveloped ds-DNA viruses

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10

Chaudhury, AM, ES Dennis, and RIS Brettell. "Gene-Expression Following T-DNA Transfer Into Plant Cells Is Aphidicolin-Sensitive." Functional Plant Biology 21, no. 2 (1994): 125. http://dx.doi.org/10.1071/pp9940125.

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A transient assay for gene-expression was used to study the early events of T-DNA transfer. Particularly, it was asked if gene expression following T-DNA transfer required DNA replication in the host cell. A β-glucuronidase gene, linked to a CaMV 35S promoter (35S-GUS, engineered so that it was inactive in Agrobacterium tumefaciens) was introduced into Nicotiana plumbaginifolia protoplasts via a disarmed supervirulent strain of Agrobacterium tumefaciens. High β-glucuronidase activity appeared after 3 days of co-cultivation. The activity required the presence of the vir functions of agrobacteri

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11

Veligura, Alina, Michael Koehler, Wolfgang Fritzsche, Peter Lytvyn, Alexandr Gorchinskyy, and Eugenia Buzaneva. "Uv induced ds(ss)-DNA damage: optical and electrical recognition." BMC Plant Biology 5, Suppl 1 (2005): S32. http://dx.doi.org/10.1186/1471-2229-5-s1-s32.

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12

Stojković, Marijana Radić, Marko Škugor, Łukasz Dudek, Jarosław Grolik, Julita Eilmes, and Ivo Piantanida. "Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives." Beilstein Journal of Organic Chemistry 10 (September 12, 2014): 2175–85. http://dx.doi.org/10.3762/bjoc.10.225.

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An investigation of the interactions of two novel and several known DBTAA–adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity relation for the studied series of compounds showed that the essential structural features for the ICD reco

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13

Koa, Helena, Murray J. Fraser, and Etta Käfer. "Endo-exonuclease of Aspergillus nidulans." Biochemistry and Cell Biology 68, no. 1 (1990): 387–92. http://dx.doi.org/10.1139/o90-054.

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Endo-exonuclease (EE) has been found in both active and inactive, but trypsin-activatable, forms in Aspergillus nidulans. Active EE was present mainly in nuclei, mitochondria, and vacuoles, while trypsin-activatable EE was mainly in the cytosol. The active form accounts for over 90% of the neutral deoxyribonuclease activity extracted from mycelia. A single strand (ss) DNA-binding EE associated with a 28 kilodalton (kDa) polypeptide was partially purified and characterized. It was found to closely resemble, in size and enzymological properties, the ss-DNA-binding EE previously purified from Neu

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14

Grueso, Elia, Rosa M. Giráldez-Pérez, Pilar Perez-Tejeda, Emilio Roldán, and R. Prado-Gotor. "What controls the unusual melting profiles of small AuNPs/DNA complexes." Physical Chemistry Chemical Physics 21, no. 21 (2019): 11019–32. http://dx.doi.org/10.1039/c9cp01162e.

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The effect of the addition of low salt concentrations on ds-DNA and ss-DNA conformational changes induced by small N-(2-mercaptopropionyl)glycine gold nanoparticles (AuNPs) is studied in detail by using different techniques. The results are correlated with the unusual melting profiles of the AuNPs/DNA complexes.

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15

Alcon, Pablo, Artur Kaczmarczyk, Tamara Sijacki, Lori Passmore, and David S. Rueda. "FANCD2-FANCI is a sliding DNA clamp that specifically recognizes ss/ds-DNA junctions." Biophysical Journal 123, no. 3 (2024): 167a. http://dx.doi.org/10.1016/j.bpj.2023.11.1112.

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16

Itriago, Humberto, Rishi K. Jaiswal, Susanne Philipp, and Marita Cohn. "The telomeric 5′ end nucleotide is regulated in the budding yeast Naumovozyma castellii." Nucleic Acids Research 50, no. 1 (2021): 281–92. http://dx.doi.org/10.1093/nar/gkab1229.

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Abstract The junction between the double-stranded and single-stranded telomeric DNA (ds–ss junction) is fundamental in the maintenance of the telomeric chromatin, as it directs the assembly of the telomere binding proteins. In budding yeast, multiple Rap1 proteins bind the telomeric dsDNA, while ssDNA repeats are bound by the Cdc13 protein. Here, we aimed to determine, for the first time, the telomeric 5′ end nucleotide in a budding yeast. To this end, we developed a permutation-specific PCR-based method directed towards the regular 8-mer telomeric repeats in Naumovozyma castellii. We find tha

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STAINS, Joseph P., Fernando LECANDA, Dwight A. TOWLER, and Roberto CIVITELLI. "Heterogeneous nuclear ribonucleoprotein K represses transcription from a cytosine/thymidine-rich element in the osteocalcin promoter." Biochemical Journal 385, no. 2 (2005): 613–23. http://dx.doi.org/10.1042/bj20040680.

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HnRNP K (heterogeneous nuclear ribonucleoprotein K) was biochemically purified from a screen of proteins co-purifying with binding activity to the osteocalcin promoter. We identify hnRNP K as a novel repressor of osteocalcin gene transcription. Overexpression of hnRNP K lowers the expression of osteocalcin mRNA by 5-fold. Furthermore, luciferase reporter assays demonstrate that overexpression of hnRNP K represses osteocalcin transcription from a CT (cytosine/thymidine)-rich element in the proximal promoter. Electrophoretic mobility-shift analysis reveals that recombinant hnRNP K binds to the C

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18

Nakai, Hiroyuki, Theresa A. Storm, and Mark A. Kay. "Recruitment of Single-Stranded Recombinant Adeno-Associated Virus Vector Genomes and Intermolecular Recombination Are Responsible for Stable Transduction of Liver In Vivo." Journal of Virology 74, no. 20 (2000): 9451–63. http://dx.doi.org/10.1128/jvi.74.20.9451-9463.2000.

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ABSTRACT Recombinant adeno-associated virus (rAAV) vectors stably transduce hepatocytes in experimental animals. Following portal-vein administration of rAAV vectors in vivo, single-stranded (ss) rAAV genomes become double stranded (ds), circularized, and/or concatemerized concomitant with a slow rise and, eventually, steady-state levels of transgene expression. Over time, at least some of the stabilized genomes become integrated into mouse chromosomal DNA. The mechanism(s) of formation of stable ds rAAV genomes from input ss DNA molecules has not been delineated, although second-strand synthe

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Yang, Bo, Xiao-Dan Zhang, Jian Li, et al. "In Situ Loading and Delivery of Short Single- and Double-Stranded DNA by Supramolecular Organic Frameworks." CCS Chemistry 1, no. 2 (2019): 156–65. http://dx.doi.org/10.31635/ccschem.019.20180011.

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Short DNA represents an important class of biomacromolecules that are widely applied in gene therapy, editing, and modulation. However, the development of simple and reliable methods for their intracellular delivery remains a challenge. Herein, we describe that seven water-soluble, homogeneous supramolecular organic frameworks (SOFs) with a well-defined pore size and high stability in water that can accomplish in situ inclusion of single-stranded (ss) and double-stranded (ds) DNA (21, 23, and 58 nt) and effective intracellular delivery (including two noncancerous and six cancerous cell lines).

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Mavlyanova, Sh Z., A. I. Ismogilov, and Zh B. Mullahanov. "Clinical and immunological characteristics of local immunity in patients with psoriasis." Terapevt (General Physician), no. 12 (December 20, 2024): 5–11. https://doi.org/10.33920/med-12-2412-01.

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The results of the ELISA study of the proinflammatory cytokine TNF-α in patients with psoriasis revealed an increase in the level by 4.4 times and secretory IgA by 2.1 times compared with the indicators of control individuals (P<0.05). Correlation analysis of secreto ry immunoglobulin A and proinflammatory cytokine TNF-α indices revealed average significance of inverse correlation with secretory IgA — r=–0.3 (P<0.05). Whereas with the level of double-stranded AAT to IgG DS — r= –0.46 and DNA SS — r=- 0.5 had inverse correlation and were statistically significant. (P <0.05). Such pict

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Xiao, Gefei, Yanling Zhao, Wuyan Huang, Liqing Hu, Guoqing Wang, and Huayu Luo. "Health economic evaluation of noninvasive prenatal testing and serum screening for down syndrome." PLOS ONE 17, no. 4 (2022): e0266718. http://dx.doi.org/10.1371/journal.pone.0266718.

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Background Down syndrome (DS), also known as trisomy 21 (T21), is the most common genetic disorder associated with intellectual disability. There are two methods commonly used for prenatal testing of DS: serum screening (SS) for biomarkers in maternal serum and noninvasive prenatal testing (NIPT) for aneuploidy by cell-free DNA (cfDNA) in maternal plasma. However, cost-effectiveness analyses of these two methods are mostly based on data derived from simulations with various models, with theoretical values calculated. In this study, we statistically analyzed clinical DS screening data and pregn

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22

Boulter, Nicky, Gregor Tevz, Betty Yu, et al. "An improved method for detection of methylated circulating tumor DNA in colorectal cancer." Journal of Clinical Oncology 37, no. 15_suppl (2019): e15120-e15120. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e15120.

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e15120 Background: Assays detecting methylated circulating tumor DNA (ctDNA) hold promise for colorectal cancer (CRC) screening, but there is a need to develop more accurate assays for early stages. In this study, we examined modifications to COLVERA (an IKZF1 and BCAT1 methylation marker qPCR assay) that added a third biomarker (IRF4) as well as introducing double stranded detection. Methods: Bisulfite converted DNA extracted from plasma collected from subjects undergoing diagnosis for CRC was assayed using either a double-stranded (ds) specific multiplexed qPCR for BCAT1 and IKZF1 detection

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Schonenberg-Meinema, D., S. Bergkamp, A. Nassar-Sheikh Rashid, et al. "POS1311 SCLERODERMA PATTERN IN NAILFOLD CAPILLARIES OF (CHILDHOOD-ONSET) SYSTEMIC LUPUS ERYTHEMATOSUS: LESSONS FROM LONGITUDINAL FOLLOW-UP." Annals of the Rheumatic Diseases 80, Suppl 1 (2021): 937.2–938. http://dx.doi.org/10.1136/annrheumdis-2021-eular.2195.

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Background:It has been suggested that a capillary scleroderma pattern in patients with systemic lupus erythematosus (SLE)-patients predisposes for clinical signs of systemic sclerosis (SSc) or overlap disease (1). However, this was previously shown not to be the case in a cross-sectional study in childhood-onset SLE (cSLE) (2).Objectives:To assess if nailfold capillary patterns in cSLE change over time and if a capillary scleroderma pattern is associated with prospective development of clinical SSc-features, higher SLE disease activity or –damage.Methods:Prospective clinical and capillaroscopy

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24

Fraccari, Raquel L., Marco Carminati, Giacomo Piantanida, Tina Leontidou, Giorgio Ferrari, and Tim Albrecht. "High-bandwidth detection of short DNA in nanopipettes." Faraday Discussions 193 (2016): 459–70. http://dx.doi.org/10.1039/c6fd00109b.

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Glass or quartz nanopipettes have found increasing use as tools for studying the biophysical properties of DNA and proteins, and as sensor devices. The ease of fabrication, favourable wetting properties and low capacitance are some of the inherent advantages, for example compared to more conventional, silicon-based nanopore chips. Recently, we have demonstrated high-bandwidth detection of double-stranded (ds) DNA with microsecond time resolution in nanopipettes, using custom-designed electronics. The electronics design has now been refined to include more sophisticated control features, such a

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Nishihara, Tadashi, Fumikiyo Nagawa, Hirofumi Nishizumi, et al. "In Vitro Processing of the 3′-Overhanging DNA in the Postcleavage Complex Involved in V(D)J Joining." Molecular and Cellular Biology 24, no. 9 (2004): 3692–702. http://dx.doi.org/10.1128/mcb.24.9.3692-3702.2004.

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ABSTRACT The postcleavage complex involved in V(D)J joining is known to possess a transpositional strand transfer activity, whose physiological role is yet to be clarified. Here we report that RAG1 and RAG2 proteins in the signal end (SE) complex cleave the 3′-overhanging structure of the synthetic coding-end (CE) DNA in two successive steps in vitro. The 3′-overhanging structure is attacked by the SE complex imprecisely, near the double-stranded/single-stranded (ds/ss) junction, and transferred to the SE. The transferred overhang is then resolved and cleaved precisely at the ds/ss junction, g

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OU-YANG, ZHONG-CAN. "THE ELASTIC THEORY OF SINGLE-MOLECULE DNA." International Journal of Modern Physics B 17, no. 01n02 (2003): 69–75. http://dx.doi.org/10.1142/s0217979203017102.

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Our recent work on the elastic responses of double- (ds) and single-stranded (ss) DNA at external force fields is reviewed. By constructing as elastic model of dsDNA in which the base-pair stacking interaction is included, we demonstrate that dsDNA entropic elasticity, cooperative extensibility, and supercoiling property can all be understood from a unified viewpoint. The base-pair stacking interaction is also found to determine the cooperativity of the stretch-induced hairpin-coil transition is ssDNA.

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Mavlyanova, Sh Z., M. S. Mutavaliev, A. I. Ismogilov, J. B. Mullakhanov, and Yu A. Alimukhamedova. "ASSESSMENT OF IgG AUTOANTIBODIES TO SINGLE-STRANDED DNA (ss-DNA) AND DOUBLE-STRANDED DNA (ds-DNA) IN PATIENTS WITH ACANTHOLYTIC PEMPHIGUS." Juvenis Scientia 6, no. 4 (2020): 57–62. http://dx.doi.org/10.32415/jscientia_2020_6_4_57-62.

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Edberg, J. C., G. A. Kujala, and R. P. Taylor. "Clearance kinetics and immunochemistry in rabbits of soluble antibody/DNA immune complexes. Effects of antibody class and DNA conformation." Journal of Immunology 139, no. 1 (1987): 180–87. http://dx.doi.org/10.4049/jimmunol.139.1.180.

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Abstract We examined the clearance kinetics in rabbits of soluble antibody/DNA immune complexes (IC) containing either IgG or IgM anti-DNA antibodies. Differences in the complement-mediated binding of these IC to rabbit blood cells (platelets) were also studied. Complexation of either double-stranded (ds) or single-stranded (ss) DNA with IgG anti-DNA tends to preclude in vivo DNA recognition mechanisms; the DNA is cleared as part of an IC at a rate slower than that of free DNA. Binding of ds- or ssDNA by IgM anti-DNA antibodies leads to formation of IC which are cleared more like free DNA, and

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Karwowski. "The Influence of (5′R)- and (5′S)-5′,8-Cyclo-2′-Deoxyadenosine on UDG and hAPE1 Activity. Tandem Lesions are the Base Excision Repair System’s Nightmare." Cells 8, no. 11 (2019): 1303. http://dx.doi.org/10.3390/cells8111303.

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DNA lesions are formed continuously in each living cell as a result of environmental factors, ionisation radiation, metabolic processes, etc. Most lesions are removed from the genome by the base excision repair system (BER). The activation of the BER protein cascade starts with DNA damage recognition by glycosylases. Uracil-DNA glycosylase (UDG) is one of the most evolutionary preserved glycosylases which remove the frequently occurring 2′-deoxyuridine from single (ss) and double-stranded (ds) oligonucleotides. Conversely, the unique tandem lesions (5′R)- and (5′S)-5′,8-cyclo-2′-deoxyadenosine

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Zhou, Xiaohuai, Irene Zolotukhin, Dong-Soo Im, and Nicholas Muzyczka. "Biochemical Characterization of Adeno-Associated Virus Rep68 DNA Helicase and ATPase Activities." Journal of Virology 73, no. 2 (1999): 1580–90. http://dx.doi.org/10.1128/jvi.73.2.1580-1590.1999.

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ABSTRACT The adeno-associated virus (AAV) nonstructural proteins Rep68 and Rep78 are site-specific DNA binding proteins, ATP-dependent site-specific endonucleases, helicases, and ATPases. These biochemical activities are required for viral DNA replication and control of viral gene expression. In this study, we characterized the biochemical properties of the helicase and ATPase activities of homogeneously pure Rep68. The enzyme exists as a monomer in solution at the concentrations used in this study (<380 nM), as judged by its mobility in sucrose density gradients. Using a primed single-stra

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Pavlovic, Mirjana, Anna Kats, Michelle Cavallo, Ran Chen, James X. Hartmann, and Yehuda Shoenfeld. "Pathogenic and Epiphenomenal Anti-DNA Antibodies in SLE." Autoimmune Diseases 2010 (2010): 1–18. http://dx.doi.org/10.4061/2010/462841.

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The discoveries of natural and the development of manufactured highly efficient catalytic antibodies (abzymes) opens the door to many practical applications. One of the most fascinating is the use of such antibodies in human therapy and prevention (vaccination), of cancer, AIDS, autoimmune diseases. A special entity of naturally occurring DNA hydrolytic anti-DNA antibodies is emerging within past decades linked to autoimmune and lymphoproliferative disorders, such as systemic lupus erythematosus (SLE), multiple sclerosis (MS), Sjogren Syndrome (SS), B - Chronic lymphocytic leucosis (B-CLL), an

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Chen, Youqiang, and Gaoquan Shi. "Fluorescence Detection and Discrimination of ss- and ds-DNA with a Water Soluble Oligopyrene Derivative." Sensors 9, no. 6 (2009): 4164–77. http://dx.doi.org/10.3390/s90604164.

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Gorbunova, Ekaterina A., Anna V. Epanchintseva, Dmitrii V. Pyshnyi, and Inna A. Pyshnaya. "Noncovalent Adsorption of Single-Stranded and Double-Stranded DNA on the Surface of Gold Nanoparticles." Applied Sciences 13, no. 12 (2023): 7324. http://dx.doi.org/10.3390/app13127324.

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Understanding the patterns of noncovalent adsorption of double-stranded nucleic acids (dsDNA) on gold nanoparticles (GNPs) was the aim of this study. It was found that the high-affinity motifs in DNA can and do act as an “anchor” for the fixation of the whole molecule on the GNP (up to 98 ± 2 single-stranded (ss)DNA molecules per particle with diameter of 13 ± 2 nm). At the same time, the involvement of an “anchor” in the intramolecular DNA interaction can negatively affect the efficiency of the formation of ss(ds)DNA–GNP structures. It has been shown that the interaction of GNP with DNA duple

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Drappa, Jorn, Lynn A. Kamen, Elena Chan, et al. "Impaired T Cell Death and Lupus-like Autoimmunity in T Cell–specific Adapter Protein–deficient Mice." Journal of Experimental Medicine 198, no. 5 (2003): 809–21. http://dx.doi.org/10.1084/jem.20021358.

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T cell–specific adaptor protein (TSAd) is a T lineage–restricted signaling adaptor molecule that is thought to participate in the assembly of intracellular signaling complexes in T cells. Previous studies of TSAd-deficient mice have revealed a role for TSAd in the induction of T cell interleukin 2 secretion and proliferation. We now show that TSAd-deficient mice are susceptible to lupus-like autoimmune disease. On the nonautoimmune-prone C57BL/6 genetic background, TSAd deficiency results in hypergammaglobulinemia that affects all immunoglobulin (Ig)G subclasses. Older C57BL/6 TSAd-deficient m

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Ye, Wei Wei, and Mo Yang. "Optimal Surface Functionalization of Nanoporous Alumina Membrane for DNA Detection." Advanced Materials Research 631-632 (January 2013): 572–75. http://dx.doi.org/10.4028/www.scientific.net/amr.631-632.572.

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This study shows the study of optimal surface functionalization of nanoporous alumina membrane for "label-free" DNA detection. Single stranded DNA was first covalently immobilized on the nanopore walls via silane-PEG-NHS linker. The remained NHS group was hydrolyzed to form PEG layer to minimize the unspecific DNA binding during hybridization process. Optimal PEG-silane linker was achieved for better DNA immobilization efficiency. Using this optofluidic device, both ss-DNA immobilization and ds-DNA hybridization were successfully monitored via UV-Vis spectrum montoring. The nanopore size effec

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Safarzadeh, Mina, and Genhua Pan. "Detection of a Double-Stranded MGMT Gene Using Electrochemically Reduced Graphene Oxide (ErGO) Electrodes Decorated with AuNPs and Peptide Nucleic Acids (PNA)." Biosensors 12, no. 2 (2022): 98. http://dx.doi.org/10.3390/bios12020098.

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The ability to detect double-stranded DNA (dsDNA) as a biomarker without denaturing it to single-stranded DNA (ss-DNA) continues to be a major challenge. In this work, we report a sandwich biosensor for the detection of the ds-methylated MGMT gene, a potential biomarker for brain tumors and breast cancer. The purpose of this biosensor is to achieve simultaneous recognition of the gene sequence, as well as the presence of methylation. The biosensor is based on reduced graphene oxide (rGO) electrodes decorated with gold nanoparticles (AuNPs) and uses Peptide Nucleic Acid (PNA) that binds to the

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Xu, Hui, Hui Li, Elisabeth Suri-Payer, Richard R. Hardy, and Martin Weigert. "Regulation of Anti-DNA B Cells in Recombination-activating Gene–deficient Mice." Journal of Experimental Medicine 188, no. 7 (1998): 1247–54. http://dx.doi.org/10.1084/jem.188.7.1247.

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Anti-DNA antibodies are regulated in normal individuals but are found in high concentration in the serum of systemic lupus erythematosus (SLE) patients and the MRL lpr/lpr mouse model of SLE. We previously studied the regulation of anti–double-stranded (ds)DNA and anti–single-stranded (ss)DNA B cells in a nonautoimmune background by generating mice carrying immunoglobulin transgenes coding for anti-DNAs derived from MRL lpr/lpr. Anti-dsDNA B cells undergo receptor editing, but anti-ssDNA B cells seem to be functionally silenced. Here we have investigated how anti-DNA B cells are regulated in r

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Heussman, Dylan J., Patrick J. Herbert, Tom Steinberg, Peter H. von Hippel, and Andrew H. Marcus. "Characterizing local conformations and conformational disorder near single-stranded (ss) - double stranded (ds) DNA replication junctions." Biophysical Journal 121, no. 3 (2022): 170a. http://dx.doi.org/10.1016/j.bpj.2021.11.1871.

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Qi, Rui, Ke Bian, Fangyi Chen, Qi Tang, Xianhao Zhou, and Deyu Li. "Sequence Dependent Repair of 1,N6-Ethenoadenine by DNA Repair Enzymes ALKBH2, ALKBH3, and AlkB." Molecules 26, no. 17 (2021): 5285. http://dx.doi.org/10.3390/molecules26175285.

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Mutation patterns of DNA adducts, such as mutational spectra and signatures, are useful tools for diagnostic and prognostic purposes. Mutational spectra of carcinogens derive from three sources: adduct formation, replication bypass, and repair. Here, we consider the repair aspect of 1,N6-ethenoadenine (εA) by the 2-oxoglutarate/Fe(II)-dependent AlkB family enzymes. Specifically, we investigated εA repair across 16 possible sequence contexts (5′/3′ flanking base to εA varied as G/A/T/C). The results revealed that repair efficiency is altered according to sequence, enzyme, and strand context (ss

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Ben-Eli, Hadas, Abraham Solomon, Doron J. Aframian, et al. "Serological and hematological characteristics of Sjogren’s syndrome and dry eye syndrome patients using a novel immune serology technique." PLOS ONE 15, no. 12 (2020): e0244712. http://dx.doi.org/10.1371/journal.pone.0244712.

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Objectives To compare hematologic and serological parameters among patients with Sjogren’s syndrome (SS), dry eye syndrome (DES) and controls, and validate a novel multiplex-serology method for identifying auto-antibodies in these populations. Methods In a clinic-based case-control study a total of 422 participants were recruited, including 91 with SS, 120 DES, and 211 controls (age and sex frequency-matched). We measured blood counts, anti-nuclear-antibodies (ANA), anti-SSA/SSB, anti-ribonucleoprotein (RNP), anti-double-stranded-DNA (DS-DNA), and rheumatoid factor (RF) using the “Immunodot” q

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He, Feng, Kevin DuPrez, Eduardo Hilario, Zhenhang Chen, and Li Fan. "Structural basis of the XPB helicase–Bax1 nuclease complex interacting with the repair bubble DNA." Nucleic Acids Research 48, no. 20 (2020): 11695–705. http://dx.doi.org/10.1093/nar/gkaa801.

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Abstract Nucleotide excision repair (NER) removes various DNA lesions caused by UV light and chemical carcinogens. The DNA helicase XPB plays a key role in DNA opening and coordinating damage incision by nucleases during NER, but the underlying mechanisms remain unclear. Here, we report crystal structures of XPB from Sulfurisphaera tokodaii (St) bound to the nuclease Bax1 and their complex with a bubble DNA having one arm unwound in the crystal. StXPB and Bax1 together spirally encircle 10 base pairs of duplex DNA at the double-/single-stranded (ds–ss) junction. Furthermore, StXPB has its ThM

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Tesmer, Valerie M., Kirsten A. Brenner, and Jayakrishnan Nandakumar. "Human POT1 protects the telomeric ds-ss DNA junction by capping the 5′ end of the chromosome." Science 381, no. 6659 (2023): 771–78. http://dx.doi.org/10.1126/science.adi2436.

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Protection of telomeres 1 (POT1) is the 3′ single-stranded overhang-binding telomeric protein that prevents an ataxia telangiectasia and Rad3–related (ATR) DNA damage response (DDR) at chromosome ends. What precludes the DDR machinery from accessing the telomeric double-stranded–single-stranded junction is unknown. We demonstrate that human POT1 binds this junction by recognizing the phosphorylated 5′ end of the chromosome. High-resolution crystallographic structures reveal that the junction is capped by POT1 through a “POT-hole” surface, the mutation of which compromises junction protection i

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Landry, Aaron P., and Huangen Ding. "The N-Terminal Domain of Human DNA Helicase Rtel1 Contains a Redox Active Iron-Sulfur Cluster." BioMed Research International 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/285791.

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Human telomere length regulator Rtel1 is a superfamily II DNA helicase and is essential for maintaining proper length of telomeres in chromosomes. Here we report that the N-terminal domain of human Rtel1 (RtelN) expressed inEscherichia colicells produces a protein that contains a redox active iron-sulfur cluster with the redox midpoint potential of −248 ± 10 mV (pH 8.0). The iron-sulfur cluster in RtelN is sensitive to hydrogen peroxide and nitric oxide, indicating that reactive oxygen/nitrogen species may modulate the DNA helicase activity of Rtel1 via modification of its iron-sulfur cluster.

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Vardevanyan, Poghos O., Valeri B. Arakelyan, Marine A. Parsadanyan, Ara P. Antonyan, Gohar G. Hovhannisyan, and Mariam A. Shahinyan. "Analysis of experimental binding curves of EtBr with single- and double-stranded DNA at small fillings." Modern Physics Letters B 28, no. 22 (2014): 1450178. http://dx.doi.org/10.1142/s0217984914501784.

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In this paper, a method that allows to analyze the binding curves of ligand ( EtBr ) with single-stranded (ss) and double-stranded (ds) DNA, when there are at least two modes of ligand binding to DNA at small fillings has been proposed. The obtained experimental binding curves for EtBr –ssDNA and EtBr –dsDNA have two clearly expressed linear regions. These curves were analyzed by two modes: Experimental points on linear regions were described by two different lines and all experimental points were described by single curve. It was revealed that the description by single curve permits obtaining

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Xiong, Ying, Bao Gao, Kesheng Wu, et al. "Fluorescence immunoassay based on the enzyme cleaving ss-DNA to regulate the synthesis of histone-ds-poly(AT) templated copper nanoparticles." Nanoscale 10, no. 42 (2018): 19890–97. http://dx.doi.org/10.1039/c8nr06175k.

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For the first time we report a novel competitive fluorescence immunoassay for the ultrasensitive detection of aflatoxin B<sub>1</sub> (AFB<sub>1</sub>) using histone-ds-poly(AT) templated copper nanoparticles (His-pAT CuNPs) as fluorescent indicators.

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Chashchina, G. V., and D. N. Kaluzhny. "Oxidative Probing of the G4 DNA Structure by ZnP1 Porphyrin within Sequences of <i>MYC</i> and <i>TERT</i> Promotors." Молекулярная биология 57, no. 3 (2023): 528–36. http://dx.doi.org/10.31857/s0026898423030035.

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The formation of G4 structures in a DNA double helix competes with the complementary strand, which can change the equilibrium G4 structures studied on single-strand models by classical structural methods. A relevant task is to develop methods for detecting and localizing G4 in extended double-stranded (ds) DNA in the promoter regions of the genome. The porphyrin derivative ZnP1 selectively binds and leads to photo-induced oxidation of guanine in G4 structures on single-stranded (ss) and dsDNA model systems. In this research, we show the oxidative effect of ZnP1 on native sequences of MYC and T

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Wloch, M. K., S. H. Clarke, and G. S. Gilkeson. "Influence of VH CDR3 arginine and light chain pairing on DNA reactivity of a bacterial DNA-induced anti-DNA antibody from a BALB/c mouse." Journal of Immunology 159, no. 12 (1997): 6083–90. http://dx.doi.org/10.4049/jimmunol.159.12.6083.

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Abstract Anti-DNA induced in BALB/c mice by immunization with bacterial (Escherichia coli) DNA resemble spontaneous anti-DNA from lupus mice in V gene use and cross-reactivity with other nuclear Ags, but lack the high V(H) CDR3 arginine content seen in anti-DNA from lupus mice. Moreover, the induced anti-DNA bind bacterial and mammalian single-stranded (ss) DNA and bacterial double-stranded (ds) DNA, but do not bind mammalian dsDNA. This reactivity profile is in contrast to that of the spontaneously arising anti-DNA of lupus mice, among which mammalian dsDNA reactive Abs are prominent. In this

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Kysil, Olena, Iryna Sporysh, Eugenia Buzaneva, et al. "The C60 fullerene molecules integration by ds-, ss-DNA molecules in fluids: Optical spectroscopy characterization of the biointerface organization." Materials Science and Engineering: B 169, no. 1-3 (2010): 85–88. http://dx.doi.org/10.1016/j.mseb.2010.01.063.

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Crnolatac, Ivo, Iva Rogan, Boris Majić, et al. "Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response." Analytica Chimica Acta 940 (October 2016): 128–35. http://dx.doi.org/10.1016/j.aca.2016.08.021.

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Wei, Yani, Luhui Wang, Yingying Zhang, and Yafei Dong. "An Enzyme- and Label-Free Fluorescence Aptasensor for Detection of Thrombin Based on Graphene Oxide and G-Quadruplex." Sensors 19, no. 20 (2019): 4424. http://dx.doi.org/10.3390/s19204424.

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An enzyme- and label-free aptamer-based assay is described for the determination of thrombin. A DNA strand (S) consisting of two parts was designed, where the first (Sa) is the thrombin-binding aptamer and the second (Se) is a G-quadruplex. In the absence of thrombin, Sa is readily adsorbed by graphene oxide (GO), which has a preference for ss-DNA rather than for ds-DNA. Upon the addition of the N-methyl-mesoporphyrin IX (NMM), its fluorescence (with excitation/emission at 399/610 nm) is quenched by GO. In contrast, in the presence of thrombin, the aptamer will bind thrombin, and thus, be sepa

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