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Journal articles on the topic 'Bp DNA fragment'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Lan, Vo Thi Thuong, and Le Thi Thanh. "Construction of DNA ladder for determination of small size DNA fragments." Vietnam Journal of Biotechnology 19, no. 3 (2021): 539–45. http://dx.doi.org/10.15625/1811-4989/13897.

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DNA marker is commonly used to determine the size of DNA fragments by electrophoresis in routine molecular biology laboratories. In this study, we report a new procedure to prepare recombinant plasmids pSY-60 which was partially digested by one restriction enzyme for generating DNA markers of 7 fragments from 60 to 420 bp. The procedure included a synthesis of 60 bp DNA fragment with EcoRI sites at both ends using PCR extension, self-ligation of the 60 bp fragments and subcloning the ligated product into plasmid, generating recombinant pSY-60. Once being cloned, 500 ng of 420 bp fragment purif

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2

Mann, C., and R. W. Davis. "Structure and sequence of the centromeric DNA of chromosome 4 in Saccharomyces cerevisiae." Molecular and Cellular Biology 6, no. 1 (1986): 241–45. http://dx.doi.org/10.1128/mcb.6.1.241-245.1986.

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The CEN4 sequences from chromosome 4 that impart mitotic stability to autonomously replicating (ARS) plasmids in yeast cells have been localized to a 1,755-base-pair (bp) fragment. This fragment could be cut in half to give two adjacent, nonoverlapping fragments, that each contained some mitotic stabilization sequences. One of the half-fragments worked as efficiently as the larger fragment from which it was derived, while the other half provided a much poorer degree of mitotic stabilization. Sequencing of 2,095 bp of DNA including this region revealed the presence of a centromere consensus seq

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3

Mann, C., and R. W. Davis. "Structure and sequence of the centromeric DNA of chromosome 4 in Saccharomyces cerevisiae." Molecular and Cellular Biology 6, no. 1 (1986): 241–45. http://dx.doi.org/10.1128/mcb.6.1.241.

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The CEN4 sequences from chromosome 4 that impart mitotic stability to autonomously replicating (ARS) plasmids in yeast cells have been localized to a 1,755-base-pair (bp) fragment. This fragment could be cut in half to give two adjacent, nonoverlapping fragments, that each contained some mitotic stabilization sequences. One of the half-fragments worked as efficiently as the larger fragment from which it was derived, while the other half provided a much poorer degree of mitotic stabilization. Sequencing of 2,095 bp of DNA including this region revealed the presence of a centromere consensus seq

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4

WU, Z., I. NAGANO, E. POZIO, and Y. TAKAHASHI. "Polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) for the identification of Trichinella isolates." Parasitology 118, no. 2 (1999): 211–18. http://dx.doi.org/10.1017/s0031182098003679.

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In the present study, polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis was developed to identify 5 species (Trichinella spiralis, Trichinella britovi, Trichinella nativa, Trichinella nelsoni and Trichinella pseudospiralis) and 3 phenotypes of uncertain taxonomic status (Trichinella T5, T6, and T8). Eleven restriction endonucleases were used to restrict 3 DNA fragments (1) a 2800 bp fragment of the 43 kDa excretory–secretory (E–S) protein gene, (2) a 1250 bp fragment amplified with the primer pair SB147A and (3) a 372 bp fragment amplified with the primer p

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5

Huang, Yanqin, Jiayi Mu, Lina Qi, et al. "Diverse fragment lengths dismiss size selection for serum cell-free DNA: a comparative study of serum and plasma samples." Clinical Chemistry and Laboratory Medicine (CCLM) 58, no. 9 (2020): 1451–59. http://dx.doi.org/10.1515/cclm-2020-0078.

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AbstractBackgroundThe objective of this study was to determine the features of fragment length for circulating cell-free DNA (cfDNA) from plasma and serum samples.MethodsPlasma and serum samples from different sources were randomly collected. Circulating cfDNA was extracted and purified by a precipitation-enriched and spin-column-based kit. The concentration of the purified DNA was immediately measured by a highly sensitive dsDNA quantitative assay, and then the fragment length was analyzed by capillary electrophoresis. The abundance of a specific fragment was estimated by the area under curve

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6

Farrow, S. M., N. S. Hawa, R. Karmali, M. Hewison, J. C. Walters, and J. L. H. O'Riordan. "Binding of the receptor for 1,25-dihydroxyvitamin D3 to the 5′-flanking region of the bovine parathyroid hormone gene." Journal of Endocrinology 126, no. 3 (1990): 355—NP. http://dx.doi.org/10.1677/joe.0.1260355.

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ABSTRACT Receptors for 1,25-dihydroxyvitamin D3 (1,25-(OH)2D3) were prepared from bovine parathyroid glands and incubated with fragments of DNA of the 5′-flanking region of the bovine parathyroid hormone (PTH) gene covering 1700 base pairs (bp) upstream of the initiation site. In filter binding assays, incubation of the DNA fragment spanning − 700 to + 50 bp with 200 μg cytosolic protein gave 288±63% (mean ± s.d.) of binding in the absence of protein. In contrast, there was no significant reaction with the −1350 to − 700 bp fragment, nor was there binding of the receptor to a fragment of DNA c

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7

Stein, Daniel C. "Transformation of Neisseria gonorrhoeae: physical requirements of the transforming DNA." Canadian Journal of Microbiology 37, no. 5 (1991): 345–49. http://dx.doi.org/10.1139/m91-056.

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The 1600-bp (base pair) fragment encoding a portion of the nalidixic acid resistant DNA gyrase, subunit B, was characterized to determine what parameters effect transformation in the gonococcus. When this DNA (pSY2) was isolated from Escherichia coli, it was able to transform a variety of gonococcal strains to resistance to nalidixic acid via DNA-mediated transformation, irrespective of their restriction–modification phenotype. Nalidixic acid resistant transformants contained no plasmid DNA sequences that corresponded to the vector, as measured by plasmid screening procedures and colony hybrid

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8

BROWN, Philip M., and Keith R. FOX. "Nucleosome core particles inhibit DNA triple helix formation." Biochemical Journal 319, no. 2 (1996): 607–11. http://dx.doi.org/10.1042/bj3190607.

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We have used DNase I footprinting to examine the formation of DNA triple helices at target sites on DNA fragments that have been reconstituted with nucleosome core particles. We show that a 12 bp homopurine target site, located 45 bp from the end of the 160 bp tyrT(46A) fragment, cannot be targeted with either parallel (CT-containing) or antiparallel (GT-containing) triplex-forming oligonucleotides when reconstituted on to nucleosome core particles. Binding is not facilitated by the presence of a triplex-binding ligand. However, both parallel and antiparallel triplexes could be formed on a tru

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9

Haab, Brian B., and Richard A. Mathies. "Optimization of Single-Molecule Fluorescence Burst Detection of ds-DNA: Application to Capillary Electrophoresis Separations of 100–1000 Basepair Fragments." Applied Spectroscopy 51, no. 10 (1997): 1579–84. http://dx.doi.org/10.1366/0003702971939136.

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Methods for optimizing the dye labeling, laser excitation, and data analysis for single-molecule fluorescence burst detection of ds-DNA have been developed and then validated through capillary electrophoresis (CE) separations of 100–1000 basepair (bp) DNA. Confocal microscopy is used to observe fluorescence bursts from individual DNA fragments labeled with the intercalation dye TO6 as they pass through the ∼ 2-μm-diameter focused laser beam. The dye concentration and laser power were optimized by studying fluorescence burst intensities from pBluescript DNA fragments. The optimal TO6 concentrat

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10

Liu, Dong, Alyson Mack, Rongchen Wang, et al. "Functional Dissection of the cis-Acting Sequences of the Arabidopsis Transposable Element Tag1 Reveals Dissimilar Subterminal Sequence and Minimal Spacing Requirements for Transposition." Genetics 157, no. 2 (2001): 817–30. http://dx.doi.org/10.1093/genetics/157.2.817.

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Abstract The Arabidopsis transposon Tag1 has an unusual subterminal structure containing four sets of dissimilar repeats: one set near the 5′ end and three near the 3′ end. To determine sequence requirements for efficient and regulated transposition, deletion derivatives of Tag1 were tested in Arabidopsis plants. These tests showed that a 98-bp 5′ fragment containing the 22-bp inverted repeat and four copies of the AAACCX (X = C, A, G) 5′ subterminal repeat is sufficient for transposition while a 52-bp 5′ fragment containing only one copy of the subterminal repeat is not. At the 3′ end, a 109-

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11

Ramadhani, Ageng Ilham, Yudit Oktanella, Wawid Purwatiningsih, Andreas Bandang Hardian, and Tatik Hernawati. "Tyrosine Kinase Gene Polymorphisms in Limousin (Bos taurus) Bull Correlation with Fresh Semen Qualities." Jurnal Veteriner 23, no. 4 (2023): 480–87. http://dx.doi.org/10.19087/jveteriner.2022.23.4.480.

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Tirosin kinase (TEK) merupakan salah satu protein pada membran plasma spermatozoa berfungsi sebagai mediator pertemuan antara spermatozoa dengan sel telur pada zona pelusida 3 (ZP3). Penelitian ini bertujuan untuk menganalisis adanya variasi gen tirosin kinase spermatozoa pada semen segar sapi limousin jantan menggunakan metode Polymerase Chain Reaction Restriction Fragment Length Polymorphism (PCR-RFLP) berdasarkan hasil fragmen DNA yang menggunakan enzim restriksi HindIII. Penelitian ini menggunakan 20 sampel darah dan semen segar yang didapat dari Balai Besar Inseminasi Buatan Singosari, Ma

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12

Raharjo, Tri Joko, Winda Cahyaningtyas, Surajiman Surajiman, Istini Istini, and Deni Pranowo. "VALIDATION OF PCR-RFLP TESTING METHOD TO DETECT PORCINE CONTAMINATION IN CHICKEN NUGGET." Indonesian Journal of Chemistry 12, no. 3 (2012): 302–7. http://dx.doi.org/10.22146/ijc.21347.

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PCR-RFLP technique to detect porcine contamination in chicken nugget has been developed and validated in this research. Various concentrations of pork were fortified during preparation of the nugget. DNA was then isolated from the nugget followed by PCR employed primers which targeted a 359 bp cytB gene fragment of mitochondrial DNA. For RFLP, the PCR product was digested by means of BamHI and BseDI enzymes. Cutting DNA fragments from nugget containing pork using BseDI enzyme produced DNA fragment with size 228 and 131 bp, while cutting with BamHI enzyme produce DNA fragments with sizes 244 an

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13

Wu, Yanduo, Yongshuang Xiao, Zhizhong Xiao, Yuting Ma, Haixia Zhao, and Jun Li. "Identification of Male-Specific Molecular Markers by Recombination of RhoGEF10 Gene in Spotted Knifejaw (Oplegnathus punctatus)." Genes 13, no. 7 (2022): 1262. http://dx.doi.org/10.3390/genes13071262.

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The spotted knifejaw (Oplegnathus punctatus) is a marine economic fish with high ecological value, food value, and fishing value, and its growth has obvious sex dimorphism. The rapid identification of its sex is beneficial to the development of sex determination and breeding. In this study, the method of comparative genomics and PCR amplification was used to further establish a rapid detection method for the recombinant RhoGEF10 gene in O. punctatus, which can quickly, accurately, and efficiently identify the sex of the O. punctatus to be tested. The homologous comparison results of male and f

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14

Ogunremi, Dele, Susan Nadin-Davis, Andrée Ann Dupras, et al. "Evaluation of a Multiplex PCR Assay for the Identification of Salmonella Serovars Enteritidis and Typhimurium Using Retail and Abattoir Samples." Journal of Food Protection 80, no. 2 (2017): 295–301. http://dx.doi.org/10.4315/0362-028x.jfp-16-167.

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ABSTRACT A multiplex PCR was developed to identify the two most common serovars of Salmonella causing foodborne illness in Canada, namely, serovars Enteritidis and Typhimurium. The PCR was designed to amplify DNA fragments from four Salmonella genes, namely, invA gene (211-bp fragment), iroB gene (309-bp fragment), Typhimurium STM 4497 (523-bp fragment), and Enteritidis SE147228 (612-bp fragment). In addition, a 1,026-bp ribosomal DNA (rDNA) fragment universally present in bacterial species was included in the assay as an internal control fragment. The detection rate of the PCR was 100% among

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15

Zhao, Qiao-Ling, Xing-Jia Shen, Liang-Jun Zhu, et al. "Characterization of CIb1 Gene Promoter from Silkworm, Bombyx mori." Zeitschrift für Naturforschung C 62, no. 11-12 (2007): 875–80. http://dx.doi.org/10.1515/znc-2007-11-1216.

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The hemolymph chymotrypsin inhibitor b1 (CIb1) of silkworm, Bombyx mori, plays an important role in innate immunity. In order to study its encoding gene CIb1, five heterogeneous promoter fragments of 844 bp, 682 bp, 516 bp, 312 bp and 82 bp in length were cloned from genomic DNA of the p50 silkworm strain. Characterization of the CIb1 promoter was performed in vitro using the firefly luciferase gene as reporter. The results showed that CIb1 promoter fragments have transcription activities in the B. mori ovary-derived BmN cell line. The 82 bp fragment (-72 to +10 nt) containing the eukaryotic c

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16

Linz, J. E., C. Katayama, and P. S. Sypherd. "Three genes for the elongation factor EF-1 alpha in Mucor racemosus." Molecular and Cellular Biology 6, no. 2 (1986): 593–600. http://dx.doi.org/10.1128/mcb.6.2.593-600.1986.

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We cloned three genes from Mucor racemosus coding for protein synthesis elongation factor 1 alpha (EF-1 alpha). A 110-base-pair (bp) EF-1 alpha-specific cDNA clone was identified by hybrid-selected translation. The nucleotide sequence of the cDNA showed significant homology to a region of the Saccharomyces cerevisiae genes for EF-1 alpha (TEF1 and TEF2). The cDNA was used to isolate an 850-bp EcoRI genomic DNA fragment containing a portion of the EF-1 alpha gene. Screening of a lambda/M. racemosus genomic DNA bank with the 850-bp EcoRI probe resulted in the identification of three DNA fragment

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17

Linz, J. E., C. Katayama, and P. S. Sypherd. "Three genes for the elongation factor EF-1 alpha in Mucor racemosus." Molecular and Cellular Biology 6, no. 2 (1986): 593–600. http://dx.doi.org/10.1128/mcb.6.2.593.

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We cloned three genes from Mucor racemosus coding for protein synthesis elongation factor 1 alpha (EF-1 alpha). A 110-base-pair (bp) EF-1 alpha-specific cDNA clone was identified by hybrid-selected translation. The nucleotide sequence of the cDNA showed significant homology to a region of the Saccharomyces cerevisiae genes for EF-1 alpha (TEF1 and TEF2). The cDNA was used to isolate an 850-bp EcoRI genomic DNA fragment containing a portion of the EF-1 alpha gene. Screening of a lambda/M. racemosus genomic DNA bank with the 850-bp EcoRI probe resulted in the identification of three DNA fragment

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18

Rahayu, Sri, Sutiman Bambang Sumitro, T. Susilawati, and Soemarno Soemarno. "IDENTIFIKASI POLIMORFISME GEN GH (GROWTH HORMONE) SAPI BALI DENGAN METODE PCR-RFLP." Berkala Penelitian Hayati 12, no. 1 (2006): 7–11. http://dx.doi.org/10.23869/bphjbr.12.1.20062.

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This study was conducted to identify polymorphism of growth hormone gene of Bali cattle. A PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) procedure was developed for determining polymorphism of growth hormone gene. The DNA was isolated from blood samples by salting out method. Total DNA were amplified with forward primer, 5’-TAGGGGAGGGTGGAAAATGGA-3’ and reverse primer, 5’-GACACCTACTCAGACAATGCG-3’. The PCR product was digested by HaeIII restriction enzyme. Result of the amplification was a specific single band with fragment 450 bp. Restriction with HaeIII restrict

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19

Hawa, N. S., J. L. H. O'Riordan, and S. M. Farrow. "Binding of 1,25-dihydroxyvitamin D3 receptors to the 5′-flanking region of the bovine parathyroid hormone gene." Journal of Endocrinology 142, no. 1 (1994): 53–60. http://dx.doi.org/10.1677/joe.0.1420053.

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Abstract To further define the binding site for receptors for 1,25(OH)2D3 (VDR) in the bovine PTH gene and to study the interactions of transcription factors with VDR, Southwestern and gel shift assays were used. Data from the former indicated binding of VDR to DNA fragments spanning the regions −451 to −348 bp and −668 to −452 bp. Studies using gel shift assays confirmed binding to the −451 to −348 bp fragment and specificity was shown by using excess concentrations of unlabelled −451 to −348 bp fragment to compete for binding, whereas excess unlabelled −347 to +50 bp did not compete. Binding

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20

Barlow, J. W., L. E. Raggatt, C. C. Drinkwater, I. G. Lyons, and R. I. Richards. "Differential binding of thyroid hormone receptors to mouse glandular kallikrein gene promoters: evidence for multiple binding regions in the mGK-6 gene." Journal of Molecular Endocrinology 3, no. 2 (1989): 79–84. http://dx.doi.org/10.1677/jme.0.0030079.

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ABSTRACT We have used a DNA-cellulose competition assay to investigate the binding of thyroid hormone receptors to fragments of the mouse glandular kallikrein genes and the human and rat GH genes. Nuclear extracts from human lymphoblastoid IM-9 cells were incubated with [125I]tri-iodothyronine ([125I]T3) and DNA-cellulose. The ability of cloned gene fragments to compete for radiolabelled receptors bound to DNA-cellulose was compared with that of DNA from pBR322. As previously observed, a 900 bp fragment from the human GH gene showed preferential binding to the thyroid hormone receptor. High-af

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21

Ruiz, Marcia T., Diamanto Matheos, Gerald B. Price, and Maria Zannis-Hadjopoulos. "OBA/Ku86: DNA Binding Specificity and Involvement in Mammalian DNA Replication." Molecular Biology of the Cell 10, no. 3 (1999): 567–80. http://dx.doi.org/10.1091/mbc.10.3.567.

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Ors-binding activity (OBA) was previously semipurified from HeLa cells through its ability to interact specifically with the 186-basepair (bp) minimal replication origin ofors8 and support ors8 replication in vitro. Here, through competition band-shift analyses, using as competitors various subfragments of the 186-bp minimal ori, we identified an internal region of 59 bp that competed for OBA binding as efficiently as the full 186-bp fragment. The 59-bp fragment has homology to a 36-bp sequence (A3/4) generated by comparing various mammalian replication origins, including the ors. A3/4 is, by

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22

SUTARNO, SUTARNO, SYARIFA ZAHRAH, OKID PARAMA ASTIRIN, ELISA HERAWATI, and AHMAD DWI SETYAWAN. "Genetic diversity of Ongole Grade, Aceh, and Sumbawa cattle based on polymorphism on ND-5 fragment mitochondrial DNA using PCR-RFLP technique." Biodiversitas Journal of Biological Diversity 20, no. 3 (2019): 783–88. http://dx.doi.org/10.13057/biodiv/d200324.

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Abstract. Sutarno, Zahrah S, Astirin OP, Herawati E, Setyawan AD. 2019. Genetic diversity of Ongole Grade, Aceh, and Sumbawa cattle based on polymorphism on ND-5 fragment mitochondrial DNA using PCR-RFLP technique. Biodiversitas 20: 783-788. Genetic diversity is the basis of livestock breeding because it can be used as an initial improvement in livestock quality through artificial selection. This study aims to determine polymorphism in ND-5 fragment of mitochondrial DNA in Ongole Grade, Aceh, and Sumbawa cattle and their genetic diversity. The total DNA from the blood of the local cattle was e

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23

Chowdhury, SMZH, AR Omar, A. Ideris, H. Bejo, and AA Jamaluddin. "Restriction endonuclease analysis of the genomes of different isolates of chicken anemia virus amplified by polymerase chain reaction." SAARC Journal of Agriculture 15, no. 2 (2018): 1–18. http://dx.doi.org/10.3329/sja.v15i2.35155.

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Four DNA fragments (fragments A, B, C and D) covering the whole genome of chicken anemia virus (CAV) were amplified enzymatically by polymerase chain reaction (PCR) using four pairs of oligonucleotide primers. The DNA fragments were amplified from each of nine CAV isolates including eight Malaysian isolates and one European isolate (Cux-1). For all nine CAV isolates, fragment A (1518 bp) was digested with one restriction enzyme, Eco130I (StyI); fragment B (926 bp) with three enzymes, Eco130I (StyI), HpaII and MboI separately; fragment C (675 bp) with also three enzymes, BsuRI (HaeIII), HinfI,

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González, Luis Miguel, Estrella Montero, Leslie J. S. Harrison, R. Michael E. Parkhouse, and Teresa Garate. "Differential Diagnosis of Taenia saginata and Taenia solium Infection by PCR." Journal of Clinical Microbiology 38, no. 2 (2000): 737–44. http://dx.doi.org/10.1128/jcm.38.2.737-744.2000.

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We have designed species-specific oligonucleotides which permit the differential detection of two species of cestodes, Taenia saginata and Taenia solium. The oligonucleotides contain sequences established for two previously reported, noncoding DNA fragments cloned from a genomic library of T. saginata. The first, which is T. saginata specific (fragment HDP1), is a repetitive sequence with a 53-bp monomeric unit repeated 24 times in direct tandem along the 1,272-bp fragment. From this sequence the two oligonucleotides that were selected (oligonucleotides PTs4F1 and PTs4R1) specifically amplifie

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Boondech, Atirada, and Sunisa Sajaw. "Checking Adulteration of Aromatic, Amylose Content and Glutinous in Rice by Using Molecular Marker." Applied Mechanics and Materials 855 (October 2016): 22–25. http://dx.doi.org/10.4028/www.scientific.net/amm.855.22.

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The purification of rice varieties were tested by using molecular markers. DNA fingerprint is the most accurate method. This research was extracted single milled rice seed varieties, which includes Proteinase K in SDS extraction buffer and 2x CTAB. Three simple sequence repeats (SSRs) markers for varietal purity test are 1) BO3, which completely co-segregate with the rice grain aroma. This primer pair amplifying a 140 bp fragment for an aromatic variety, KDML105 and a 130 bp fragment for a non-aromatic variety, RD29, 41, 49 and rice berry, respectively. 2) RM190, which is closely linked to wax

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MIN, WONGI, HEE-JONG WOO, CHUL-SANG LEE, et al. "307-bp Fragment inH0XA7Upstream Sequence Is Sufficient for Anterior Boundary Formation." DNA and Cell Biology 17, no. 3 (1998): 293–99. http://dx.doi.org/10.1089/dna.1998.17.293.

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Huong, Bui Thi Mai, Ha Van Huan, and Le Tho Son. "Identification of dna barcode sequence of hybrid eucalyptus UP99 (E. urophylla x E. pellita) and UP95 (E. urophylla x E. pellita) to identify plant varieties." Journal of Forestry Science and Technology 8, no. 2 (2023): 36–46. http://dx.doi.org/10.55250/jo.vnuf.8.2.2023.036-046.

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The hybrid Eucalyptus UP99 (E. urophylla x E. pellita) and UP95 (E. urophylla x E. pellita) were recognized as a high economic value species according to Decision 65/QĐ-BNN-LN on January 11th in 2013. However, it is very difficult to the famer in identifying these species by morphological observation. Therefore, this study aimed to develop a method using DNA barcode fragments to identify the hybrid Eucalyptus UP99 and UP95. The total genomic DNA was extracted from leaf samples of UP99 and UP95 and was used to amplify the DNA barcodes (matK, rbcL, trnH-psbA, ITS and ITS2) by PCR. The results sh

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Zhang, A. W., G. L. Hartman, B. Curio-Penny, W. L. Pedersen, and K. B. Becker. "Molecular Detection of Diaporthe phaseolorum and Phomopsis longicolla from Soybean Seeds." Phytopathology® 89, no. 9 (1999): 796–804. http://dx.doi.org/10.1094/phyto.1999.89.9.796.

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Species-specific detection of Diaporthe phaseolorum and Phomopsis longicolla from soybean seeds was accomplished using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and TaqMan chemistry. To use these detection systems, fungal DNA was released from soybean seed coats using an ultrasonic processor to break the cells. DNA fragment lengths ranged from 200 to 1,200 base pairs (bp), with the majority of fragments <500 bp. Based on DNA sequences of the internal transcribed spacer (ITS) regions of ribosomal DNA, three TaqMan primer/probe sets were designed. Primer/pr

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Cottarel, G., J. H. Shero, P. Hieter, and J. H. Hegemann. "A 125-base-pair CEN6 DNA fragment is sufficient for complete meiotic and mitotic centromere functions in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 8 (1989): 3342–49. http://dx.doi.org/10.1128/mcb.9.8.3342-3349.1989.

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Saccharomyces cerevisiae centromeres contain a conserved region ranging from 111 to 119 base pairs (bp) in length, which is characterized by the three conserved DNA elements CDEI, CDEII, and CDEIII. We isolated a 125-bp CEN6 DNA fragment (named ML CEN6) containing only these conserved elements and assayed it completely separated from its chromosomal context on circular minichromosomes and on a large linear chromosome fragment. The results show that this 125-bp CEN6 DNA fragment is by itself sufficient for complete mitotic and meiotic centromere functions.

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Cottarel, G., J. H. Shero, P. Hieter, and J. H. Hegemann. "A 125-base-pair CEN6 DNA fragment is sufficient for complete meiotic and mitotic centromere functions in Saccharomyces cerevisiae." Molecular and Cellular Biology 9, no. 8 (1989): 3342–49. http://dx.doi.org/10.1128/mcb.9.8.3342.

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Saccharomyces cerevisiae centromeres contain a conserved region ranging from 111 to 119 base pairs (bp) in length, which is characterized by the three conserved DNA elements CDEI, CDEII, and CDEIII. We isolated a 125-bp CEN6 DNA fragment (named ML CEN6) containing only these conserved elements and assayed it completely separated from its chromosomal context on circular minichromosomes and on a large linear chromosome fragment. The results show that this 125-bp CEN6 DNA fragment is by itself sufficient for complete mitotic and meiotic centromere functions.

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Mouliere, Florent, Dineika Chandrananda, Anna M. Piskorz, et al. "Enhanced detection of circulating tumor DNA by fragment size analysis." Science Translational Medicine 10, no. 466 (2018): eaat4921. http://dx.doi.org/10.1126/scitranslmed.aat4921.

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Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for noninvasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 patients with cancer using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized

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Wakasa, Y., R. Ishikawa, M. Niizeki, et al. "Majin: A Miniature DNA Element Associated with the Genomes of Pome Fruit Trees." HortScience 38, no. 1 (2003): 17–20. http://dx.doi.org/10.21273/hortsci.38.1.17.

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Sequencing of the sequence tagged site-DNA marker fragments linked to the fruit skin-color gene in apple revealed two fragments containing insertions that are associated with yellow skin color, and are alleles of the red skin gene (Rf). One fragment resulted from the insertion of a 76-bp inverted repeat, whereas the 163 bp in the other fragment was characterized as a mobile element because of the presence of target site duplication. A database search found this latter element in the 5' flanking regions or intron of six apple genes. DNA blot analysis revealed that the element is highly reiterat

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He, Huoguang, Bin Wu, Min Xiong, Yang Li, Wenhua Wu, and Xingguo Wang. "Gene cloning, structural gene and promoter identification, and active assay of the phosphatidylcholine synthase of Pseudomonas sp. strain 593." Canadian Journal of Microbiology 57, no. 10 (2011): 785–94. http://dx.doi.org/10.1139/w11-073.

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Pseudomonas sp. strain 593, a soil bacterium, is able to use exogenous choline to synthesize phosphatidylcholine via phosphatidylcholine synthase (Pcs). A 2020 bp DNA fragment that hybridized to a Pcs probe was cloned. This fragment contained a large open reading frame (ORF) with two potential ATG start sites that would encode for 293 and 231 amino acid proteins. Fragments containing the two ORFs encoded Pcs when they were inserted into the expression vector pET23a and expressed under the control of the T7 promoter in Escherichia coli BL21(DE3) pLysS. However, when the two ORFs were inserted i

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Li, Xiaolei, Weiping Zeng, Jing Liao, Zhenbiao Liang, Shuhua Huang, and Zhi Chao. "DNA Barcode-Based PCR-RFLP and Diagnostic PCR for Authentication of Jinqian Baihua She (Bungarus Parvus)." Evidence-Based Complementary and Alternative Medicine 2015 (2015): 1–7. http://dx.doi.org/10.1155/2015/402820.

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We established polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and diagnostic PCR based on cytochrome C oxidase subunit I (COI) barcodes ofBungarus multicinctus, genuine Jinqian Baihua She (JBS), and adulterant snake species. The PCR-RFLP system utilizes the specific restriction sites ofSpeI andBstEII in the COI sequence ofB. multicinctusto allow its cleavage into 3 fragments (120 bp, 230 bp, and 340 bp); the COI sequences of the adulterants do not contain these restriction sites and therefore remained intact after digestion withSpeI andBstEII (except for that ofZ

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Chang, S., ME Reid, J. Conboy, YW Kan, and N. Mohandas. "Molecular characterization of erythrocyte glycophorin C variants." Blood 77, no. 3 (1991): 644–48. http://dx.doi.org/10.1182/blood.v77.3.644.644.

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Abstract Human erythrocyte glycophorin C plays a functionally important role in maintaining erythrocyte shape and regulating membrane mechanical stability. Immunochemical and serologic studies have identified a number of glycophorin C variants that include the Yus, Gerbich, and Webb phenotypes. We report here the molecular characterization of these variants. Amplification of glycophorin C mRNA from the Yus phenotype, using two oligonucleotide primers that span the coding domain, generated a 338-bp fragment compared with a 395-bp fragment generated by amplification of normal glycophorin C mRNA.

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Chang, S., ME Reid, J. Conboy, YW Kan, and N. Mohandas. "Molecular characterization of erythrocyte glycophorin C variants." Blood 77, no. 3 (1991): 644–48. http://dx.doi.org/10.1182/blood.v77.3.644.bloodjournal773644.

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Human erythrocyte glycophorin C plays a functionally important role in maintaining erythrocyte shape and regulating membrane mechanical stability. Immunochemical and serologic studies have identified a number of glycophorin C variants that include the Yus, Gerbich, and Webb phenotypes. We report here the molecular characterization of these variants. Amplification of glycophorin C mRNA from the Yus phenotype, using two oligonucleotide primers that span the coding domain, generated a 338-bp fragment compared with a 395-bp fragment generated by amplification of normal glycophorin C mRNA. Sequenci

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AN, J., N. BEAUCHEMIN, J. ALBANESE, T. O. ABNEY, and A. K. SULLIVAN. "Use of a Rat cDNA Probe Specific for the Y Chromosome to Detect Male‐Derived Cells." Journal of Andrology 18, no. 3 (1997): 289–93. http://dx.doi.org/10.1002/j.1939-4640.1997.tb01921.x.

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ABSTRACT: A cDNA probe that exhibits specificity for the rat Y chromosome was generated by using a set of primers specific to the murine Sry gene, the sex‐determining region of the Y chromosome. A 459‐base pair (bp) DNA fragment was obtained by polymerase chain reaction (PCR) amplification from male, but not female, rat genomic DNA (EMBL Nucleotide Sequence Database accession number X89730). This DNA fragment was purified, cloned using a vector, and digested with EcoR1 to yield a 270‐bp DNA fragment. This 270‐bp cDNA fragment, when used as a probe in Southern blot analysis of rat DNA, was obse

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Ferrier, Sarah Tadhg, Erica Mandato, Alexandra Bartolomucci, Thupten Tsering, Shuk On Annie Leung, and Julia Valdemarin Burnier. "Abstract 5596: Cell free DNA levels and fragmentation patterns in different liquid biopsy analytes (blood, urine and vaginal fluid) in cervical cancer patients." Cancer Research 83, no. 7_Supplement (2023): 5596. http://dx.doi.org/10.1158/1538-7445.am2023-5596.

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Abstract Background: Cervical cancer (CC) is the 4th most commonly diagnosed cancer among women, with approximately 528,000 new cases annually. Current screening approaches for this disease have certain limitations; Pap tests require dedicated cytopathology infrastructure, while human papillomavirus (HPV) DNA testing may lead to invasive procedures in patients with transient infection. Liquid biopsy has emerged as a minimally invasive approach to detect and monitor disease progression and treatment response. We and others have previously demonstrated the clinical utility of circulating tumor (

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Ali, B. A., A. A. El-Hanafy, and H. H. Salem. "Genetic biodiversity studies on IGFBP-3 gene in Egyptian sheep breeds." Biotehnologija u stocarstvu 25, no. 1-2 (2009): 101–9. http://dx.doi.org/10.2298/bah0902101a.

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The insulin-like growth factor binding protein-3 (IGFBP-3) gene is a structural gene associated with the growth and development of the animals. The present investigation was carried out to study DNA polymorphism by PCR-RFLP of IGFBP-3 gene in four Egyptian local sheep breeds and its comparison with Indian sheep breeds. Genomic DNA was isolated from a total of 20 animals from four Egyptian breeds of sheep namely Rahmani, Ossimi, Awassi, and Barki. A fragment of IGFBP-3 gene, comprising of a part of exon 2, complete intron 2, exon 3, and a part of intron 3, was amplified. The amplified fragment

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Cing, Jap Mai, Djarot Sasongko Hami Seno, and Tri Joko Santoso. "Identification of Aroma Gene (Mutated badh2) and Properties of Aroma on Aromatic BC₅F₂ Ciherang." Current Biochemistry 2, no. 1 (2015): 42–51. http://dx.doi.org/10.29244/cb.2.1.42-51.

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Aromatic rice varieties have some weaknesses such as low productivity, and less resistant to pests and diseases. This study aimed to obtain homozygous strain of BC5F2 Ciherang aromatic through the identification of aroma gene (mutated badh2) and properties of the aroma. Ciherang paddy (nonaromatic paddy) was used as the female parent, whereas Mentik Wangi paddy (aromatic paddy) was used as the male parent. The experiment was conducted in BC5F2 because it is expected to generate plants with properties 98.4% close to female parent. The DNA from five strains of paddy plants BC5F2Ciherang X Mentik

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KHALED, K. A. M., R. M. M. HABIBA, J. A. BASHASHA, C. R. AZZAM, and M. H. ABDEL-AZIZ. "IN SILICO AND GENETIC ANALYSIS RELATED TO TILLERING ABILITY IN MAIZE." SABRAO Journal of Breeding and Genetics 55, no. 1 (2023): 156–62. http://dx.doi.org/10.54910/sabrao2023.55.1.15.

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Maize developed from its ancestor, teosinte, about 10,000 years ago. The evolution has gone from teosinte with multiple tillers to single-tiller maize plants. An investigation took place to identify and sequence genes related to tillering ability in maize and perform In silico analysis. Mating proceeded by manual pollination between the commercial hybrid SC2031 of maize (Zea mays L.) and the teosinte genotype Domiata (Durra rayyana). The parents, F1 hybrids, and their F2 progenies gained evaluation for tillering ability. The SC2031 (low or no-tillers) exhibited fragments ranging from 75 to 420

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Choo, Quok-Cheong, Mohd-Razip Samian, and Nazalan Najimudin. "Phylogeny and Characterization of Three nifH-Homologous Genes from Paenibacillus azotofixans." Applied and Environmental Microbiology 69, no. 6 (2003): 3658–62. http://dx.doi.org/10.1128/aem.69.6.3658-3662.2003.

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ABSTRACT In this paper, we report the cloning and characterization of three Paenibacillus azotofixans DNA regions containing genes involved in nitrogen fixation. Sequencing analysis revealed the presence of nifB1H1D1K1 gene organization in the 4,607-bp SacI DNA fragment. This is the first report of linkage of a nifB open reading frame upstream of the structural nif genes. The second (nifB2H2) and third (nifH3) nif homologues are confined within the 6,350-bp HindIII and 2,840-bp EcoRI DNA fragments, respectively. Phylogenetic analysis demonstrated that NifH1 and NifH2 form a monophyletic group

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Elledge, S. J., and R. W. Davis. "Identification of the DNA damage-responsive element of RNR2 and evidence that four distinct cellular factors bind it." Molecular and Cellular Biology 9, no. 12 (1989): 5373–86. http://dx.doi.org/10.1128/mcb.9.12.5373-5386.1989.

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The RNR2 gene encodes the small subunit of ribonucleotide reductase, the enzyme that catalyzes the first step in the pathway for the production of the deoxyribonucleotides needed for DNA synthesis. Transcription of this gene is induced approximately 20-fold in response to environmental stimuli that damage DNA or block DNA replication. Deletion and subcloning analysis identified two, and possibly three, upstream activating sequences (UAS) and one repressing (URS) element in the RNR2 regulatory region. A 42-base-pair (bp) fragment from this region was found to be necessary for proper regulation

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Elledge, S. J., and R. W. Davis. "Identification of the DNA damage-responsive element of RNR2 and evidence that four distinct cellular factors bind it." Molecular and Cellular Biology 9, no. 12 (1989): 5373–86. http://dx.doi.org/10.1128/mcb.9.12.5373.

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The RNR2 gene encodes the small subunit of ribonucleotide reductase, the enzyme that catalyzes the first step in the pathway for the production of the deoxyribonucleotides needed for DNA synthesis. Transcription of this gene is induced approximately 20-fold in response to environmental stimuli that damage DNA or block DNA replication. Deletion and subcloning analysis identified two, and possibly three, upstream activating sequences (UAS) and one repressing (URS) element in the RNR2 regulatory region. A 42-base-pair (bp) fragment from this region was found to be necessary for proper regulation

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Sharma, Ranjana, Trevor W. Alexander, S. Jacob John, Robert J. Forster, and Tim A. McAllister. "Relative stability of transgene DNA fragments from GM rapeseed in mixed ruminal cultures." British Journal of Nutrition 91, no. 5 (2004): 673–81. http://dx.doi.org/10.1079/bjn20041100.

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The use of transgenic crops as feeds for ruminant animals has prompted study of the possible uptake of transgene fragments by ruminal micro-organisms and/or intestinal absorption of fragments surviving passage through the rumen. The persistence in buffered ruminal contents of seven different recombinant DNA fragments from GM rapeseed expressing the5-enolpyruvylshikimate-3-phosphate synthase(EPSPS) transgene was tracked using PCR. Parental and transgenic (i.e. glyphosphate-tolerant; Roundup Ready®, Monsanto Company, St Louis, MO, USA) rapeseed were incubated for 0, 2, 4, 8, 12, 24 and 48 h as w

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Parenrengi, Andi, Sulaeman Sulaeman, Emma Suryati, and Andi Tenriulo. "KARAKTERISASI GENETIKA RUMPUT LAUT Kappaphycus alvarezii YANG DIBUDIDAYAKAN DI SULAWESI SELATAN." Jurnal Riset Akuakultur 1, no. 1 (2016): 1. http://dx.doi.org/10.15578/jra.1.1.2006.1-11.

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Karakterisasi genetika rumput laut Kappaphycus alvarezii telah dilakukan dengan menggunakan teknik Random Amplified Polymorphic DNA (RAPD) dengan tujuan untuk mengetahui variasi genetika rumput laut K. alvarezii dari beberapa lokasi budi daya di Sulawesi Selatan yakni Polmas, Pinrang, Takalar, dan Bantaeng. Sampel dipreservasi dengan menggunakan larutan TNES-Urea sebelum ekstraksi DNA. Ekstraksi genom DNA dilakukan dengan menggunakan metode konvensional fenol-khloroform. Amplifikasi DNA dilakukan dengan teknik Polymerase Chain Reaction (PCR). Untuk dokumentasi riset, hasil PCR dielektroforesis

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Yoo, H. S., and T. G. Cooper. "The DAL7 promoter consists of multiple elements that cooperatively mediate regulation of the gene's expression." Molecular and Cellular Biology 9, no. 8 (1989): 3231–43. http://dx.doi.org/10.1128/mcb.9.8.3231-3243.1989.

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Expression of the allantoin system genes in Saccharomyces cerevisiae is induced by allophanate or its analog, oxalurate. This work provides evidence for the involvement of distinct types of cis-acting elements in the induction process. The first element was found to have the properties of an upstream activation sequence (UAS). This element was localized to a 16-base-pair (bp) DNA fragment containing a short 5-bp sequence that occurred repeatedly in the upstream region of DAL7. When present in two or more copies, the 16-bp fragment supported high-level beta-galactosidase production in a CYC1-la

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Yoo, H. S., and T. G. Cooper. "The DAL7 promoter consists of multiple elements that cooperatively mediate regulation of the gene's expression." Molecular and Cellular Biology 9, no. 8 (1989): 3231–43. http://dx.doi.org/10.1128/mcb.9.8.3231.

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Expression of the allantoin system genes in Saccharomyces cerevisiae is induced by allophanate or its analog, oxalurate. This work provides evidence for the involvement of distinct types of cis-acting elements in the induction process. The first element was found to have the properties of an upstream activation sequence (UAS). This element was localized to a 16-base-pair (bp) DNA fragment containing a short 5-bp sequence that occurred repeatedly in the upstream region of DAL7. When present in two or more copies, the 16-bp fragment supported high-level beta-galactosidase production in a CYC1-la

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FERNÁNDEZ, ALICIA, TERESA GARCÍA, ISABEL GONZÁLEZ, et al. "Polymerase Chain Reaction–Restriction Fragment Length Polymorphism Analysis of a 16S rRNA Gene Fragment for Authentication of Four Clam Species." Journal of Food Protection 65, no. 4 (2002): 692–95. http://dx.doi.org/10.4315/0362-028x-65.4.692.

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Specific identification of four clam species, Ruditapes decussatus (grooved carpet shell), Venerupis pullastra (pullet carpet shell), Ruditapes philippinarum (Japanese carpet shell), and Venerupis rhomboides (yellow carpet shell), was achieved by polymerase chain reaction–restriction fragment length polymorphism analysis of a fragment of the mitochondrial 16S rRNA gene. Amplification of DNA isolated from the foot muscle produced fragments of 511 bp for V. pullastra, 523 bp for R. decussatus, 545 bp for R. philippinarum, and 502 bp for V. rhomboides. The restriction profiles obtained by agarose

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Yang, Ze Xiao, Gui Li Li, Yin Wang, et al. "Primary Establishment of LAMP Method for Cyprinid Herpesvirus 2 Detection." Applied Mechanics and Materials 602-605 (August 2014): 1823–28. http://dx.doi.org/10.4028/www.scientific.net/amm.602-605.1823.

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A new loop-mediated isothermal amplification (LAMP) method for the detection of Cyprinid herpesvirus 2 (CyHV-2) was developed. Following the synthesis in vitro of a 413 bp DNA fragment of CyHV2 DNA-dependent DNA polymerase gene by overlap extension PCR using 11 overlapping oligo primers designed according to the gensome sequences information of CyHV2 published in GenBank, a set of 6 LAMP primers were designed based on the synthesized DNA fragment, and the LAMP assay was primarily established after preparation of target gene fragments, optimization of reaction conditions, products identificatio

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