scholarly journals The Efficiency of Long Primers Compared to The Short Primer for RAPD Technique in Date Palm

2022 ◽  
Vol 16 (1) ◽  
pp. 1
Author(s):  
Aisyah Mohd Ismail ◽  
Farida Zuraina Mohd Yusof

Random Amplified Polymorphic DNA (RAPD) applies single arbitrary short primers (8-12nucleotides) to produce many amplified discrete DNA. Limited reports and studies were done onthe use of long primers (over 12 bases). This study was performed to investigate the potential valueof long primers (15-21 bases) for generating RAPD polymorphisms. We compared both short andlong primers in RAPD assays of two date palm cultivars grown in Malaysia: Ajwa and Barhi. Thenumber of produced polymorphic fragments ranged in order from 2 and 38 bands for short andlong primers in Ajwa. Meanwhile, more polymorphic fragments were generated by long primersin Barhi, which were 50 and only five bands for short primers. 18-mer GY107 and 20-mer CO4primers yielded 100% polymorphism in Ajwa and Barhi, respectively. Moreover, long primersproduced more DNA fragments and a wider range of DNA fragment sizes (from 140-1600 bp,with respect to 300-1000 bp obtained with 10-mer primers). Hence, a significant correlation wasobserved between primer length and the number of polymorphic fragments within the long primergroup, suggesting that increasing primer length above 15 bases may demonstrate enhancedproduction of more polymorphism.

1995 ◽  
Vol 120 (5) ◽  
pp. 730-733 ◽  
Author(s):  
J. Yu ◽  
W.K. Gu ◽  
R. Provvidenti ◽  
N.F. Weeden

Two random amplified polymorphic DNA (RAPD) markers linked to En, the gene conferring resistance to pea enation mosaic virus in pea, were identified and the DNA fragments were cloned and partially sequenced. Allele-specific associated primers for each cloned DNA fragment were developed and used in screening F2 populations. One marker, P256900, mapped very near Adh-1, about 6 cM from En. The other marker, B500400, was located about 8 cM from En on the same side as P256900.


2020 ◽  
Vol 4 (2) ◽  
pp. 57-62
Author(s):  
IRFAN MARTIANSYAH ◽  
NURHAIMI HARIS ◽  
TATI HUSNIYATI ◽  
EDI DJAUHARI PURWAKUSUMAH

The rubber seeds are insufficient for producing rootstocks to rubber grafting. It can be overcome by an in vitro micro-cutting culture technique developed in the Indonesian Research Institute for Biotechnology and Bioindustry (IRIBB). However, the origin clone of 57 rubber genotypes used as an explant source in vitro micro-cutting culture is not recognized. The study was to investigate the 57 genotypes that came from mixed GT 1, PB 260, and RRIM 600 as parent clones. We investigated using seven primers of Random Amplified Polymorphic DNA (RAPD), i.e., OPA 02, OPA 07, OPA 15, OPB 04, OPC 05, OPC 11, and OPC 20. The qualitative analyzed by electrophoresis 1% gel agarose. A total of 47 DNA fragments produced with an average of 7 fragments per primer. OPA 02 generated of 13 fragments, whereas OPB 04 only one fragment. The DNA fragment pattern shows the presence of polymorphism. The genetic similarity coefficients obtained in the range of 62-96%. The highest genetic similarity (96%) is genotype 70 and 78. It recognized that 42 genotypes from 57 rubber genotypes had the closest relationship with PB 260 clones. Furthermore, six genotypes had a significant growth response as an explant in vitro micro-cutting culture.


1997 ◽  
Vol 82 (3) ◽  
pp. 389-398 ◽  
Author(s):  
M.T. MOMOL ◽  
E.A. MOMOL ◽  
W.F. LAMBOY ◽  
J.L. NORELLI ◽  
S.V. BEER ◽  
...  

2020 ◽  
Vol 58 (4) ◽  
pp. 527-532 ◽  
Author(s):  
Jee-Soo Lee ◽  
Miyoung Kim ◽  
Moon-Woo Seong ◽  
Han-Sung Kim ◽  
Young Kyung Lee ◽  
...  

AbstractBackgroundChoosing the specimen type is the first step of the pre-analytical process. Previous reports suggested plasma as the optimal specimen for circulating tumor DNA (ctDNA) analysis. However, head-to-head comparisons between plasma and serum using platforms with high analytical sensitivity, such as droplet digital polymerase chain reaction (ddPCR), are limited, and several recent studies have supported the clinical utility of serum-derived ctDNA. This study aimed to compare the DNA profiles isolated from plasma and serum, characterize the effects of the differences between specimens on ctDNA measurement, and determine the major contributors to these differences.MethodsWe isolated cell-free DNA (cfDNA) from 119 matched plasma/serum samples from cancer patients and analyzed the cfDNA profiles by DNA fragment sizing. We then assessed KRAS mutations in ctDNA from matched plasma/serum using ddPCR.ResultsThe amount of large DNA fragments was increased in serum, whereas that of cfDNA fragments (<800 bp) was similar in both specimens. ctDNA was less frequently detected in serum, and the KRAS-mutated fraction in serum was significantly lower than that in plasma. The differences in ctDNA fractions between the two specimen types correlated well with the amount of large DNA fragments and white blood cell and neutrophil counts.ConclusionsOur results provided detailed insights into the differences between plasma and serum using DNA fragment sizing and ddPCR, potentially contributing to ctDNA analysis standardization. Our study also suggested that using plasma minimizes the dilution of tumor-derived DNA and optimizes the sensitivity of ctDNA analysis. So, plasma should be the preferred specimen type.


2020 ◽  
Vol 36 (11) ◽  
pp. 3322-3326
Author(s):  
Michael Schwarz ◽  
Marius Welzel ◽  
Tolganay Kabdullayeva ◽  
Anke Becker ◽  
Bernd Freisleben ◽  
...  

Abstract Summary The development of de novo DNA synthesis, polymerase chain reaction (PCR), DNA sequencing and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this article, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms. Furthermore, MESA can be used to simulate errors during synthesis, PCR, storage and sequencing processes. Availability and implementation MESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.


2016 ◽  
Vol 75 (1) ◽  
Author(s):  
Djoko SANTOS ◽  
Agustina A. HANDAYAN ◽  
Sukarti MOELJOPAWIRO

SummaryPromoter is a regulator of geneexpression for a phenotype or trait carried bythe gene. In the structure, a promoter locatedbeyond the 5’ end of the open reading frame ofthe gene on which its expression is regulated.This research aimed to isolate the DNAfragment flanking TcLFY at the 5’ end and toanalyze whether the fragment has charac-teristics of the promoter, primarily the coremotifs of promoter. Using Genome Walkingtechnique, DNA fragments flanking the TcLFYgene at its 5’ end was isolated. Analysis of theDNA sequence was done using onlinecomputer software accessible through web sitewww.softberry.com and an entry sequence ofthe flanking DNA fragment along with the 2.5kb TcLFY sequence. The result indicated thatthe flanking fragment has core motifs for apromoter at proper positions, which are TATAbox at position –80, CAT boxes (CCAAT) at -387 and –626, and GC boxes that are known asUAS were found at the -323 and –537positions. To obtain a conclusive result, thispromoter sequence needs to be furtherexamined to confirm its function.RingkasanPromoter merupakan pengendali ekspresigen untuk memunculkan fenotipe atau karakteryang dibawa oleh gen tersebut. Di dalamstrukturnya, promoter umumnya terletak didaerah ujung 5’ gen yang dikendalikanekspresinya. Tujuan penelitian ini adalahmendapatkan fragmen DNA yang mengapitgen pengendali pembungaan kakao (TcLFY)dan menganalisisnya apakah memilikikarakteristik promoter, yaitu mengandungmotif-motif inti (core motifs) dari promoter.Dengan teknik Genome Walking, fragmenDNA pengapit gen TcLFY di ujung 5’ dapatdiisolasi. Analisis sekuen menggunakanperangkat lunak komputer online (www.softberry.com) dengan input data fragmentersebut ditambah gen TcLFY 2,5 kb dibawahnya, mengindikasikan adanya beberapamotif inti promoter pada posisi yang sesuai,yaitu kotak TATA pada lokasi –80, kotak CAT(CCAAT) di posisi -387 dan –626, dan kotakGC yang merupakan UAS dijumpai padalokasi -323 dan –537. Untuk memperoleh hasilyang bersifat konklusif, sekuen promoter inimasih perlu diuji fungsinya.


2009 ◽  
Vol 64 (7-8) ◽  
pp. 581-589 ◽  
Author(s):  
Pin Lv ◽  
Xiangshan Zhou ◽  
Jinhua You ◽  
Bang-Ce Ye ◽  
Yuanxing Zhang

DNA extraction from food is always problematic especially from highly processed samples which contain only trace amounts of severely degraded DNA fragments. In this work, to extract trace amounts of small DNA fragments of the traditional Chinese medicine (TCM) colla corii asini derived from highly processed Equus asinus skin, three strategies were compared for its authentication. With some optimizations, the modified QIAquick spin column method achieved higher DNA yield and purity in comparison with the “SDS/proteinase K” method and the “Wizard magnetic DNA purification system for food” method. Further studies showed that at least 0.4 g colla corii asini was needed to obtain enough DNA extracts for PCR-based detection by the method and only amplicons of less than 100 bp could be generated from the DNA extracts which confirmed the efficiency of the method in small DNA fragment extraction. The DNA obtained by this method was suitable to be used in PCR-based authentications.


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