scholarly journals A Customized Simulated Annealing Suitable for Primer Design in Polymerase Chain Reaction Processes

10.5772/46941 ◽  
2010 ◽  
Author(s):  
Luciana ◽  
Maria Do Carmo Nicoletti ◽  
Said Sadique ◽  
Maria Emlia Machado Telles Walter
Keyword(s):  
Polymerase Chain Reaction ◽  
Simulated Annealing ◽  
Primer Design ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Reaction Processes

scholarly journals RANCANGAN PRIMER SPESIFIK GEN MACROPHAGE MANNOSE RECEPTOR (MMR) UNTUK POLYMERASE CHAIN REACTION (PCR) DAN SEKUENSING DEOXYRIBO NUCLEIC ACID (DNA)

2018 ◽  
Vol 22 (2) ◽  
pp. 158
Author(s):  
Yani Triyani ◽  
Nurizzatun Nafsi ◽  
Lelly Yuniarti ◽  
Nanan Sekarwana ◽  
Endang Sutedja ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequencing ◽  
Mannose Receptor ◽  
Primer Design ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Specific Pcr ◽  
Polymerase Chain ◽  
Dna Sequencing Analysis

The order (sequencing) determinationof DeoxyribonucleicAcid (DNA) bases is the gene’s most basic information, using the methodof Polymerase Chain Reaction (PCR) as its stage. A key factor of successful detection by PCR is specific PCR primer design choice. Thedetection of diversity of Mycobacterium Mannose Receptor (MMR) gene, responsible for recognizing mannosylated antigen structureof Mycobacterium tuberculosis (M.tb) by DNA sequencing of exon 7 chromosome 10p12, related to susceptiblity for PulmonaryTuberculosis(TB), was first performed in China in 2012. The purpose of this study was to find specific primerfromboth design originatedfrom the research in China/primer I and my own design/primer IIby using Primer3 software. This study was based on 10 healthy subjectsand was a preliminary study of a research titled. The Relationship of Single Nucleotide Polymorphisms (SNPs) of Macrophage MannoseReceptor Gene to Pulmonary Tuberculosis Cases. The examination materials consist of 3 mL of EDTA blood and DNA extraction from itsbuffy coat. The resulting DNA was processed by PCR to amplify MMR gene with primer I and II. The primer I successfully amplified DNAfragments up to 780bp while primer II only 329 bp. The MMR gene DNA sequencing analysis was performed on the amplification resultof both kinds primers by using DNA Baser and Ensembl−BLAST software. The results were different, DNA sequencing result by using theprimer I was found in several chromosomes and also in several loci. Whereas, by using the primer II, it was only found in chromosome10 and in the same locus. Based on this study, it can be concluded that the specific primer design is one of the most important factorsin the success of DNA sequencing.

Specific primer design for the polymerase chain reaction

2013 ◽  
Vol 35 (10) ◽  
pp. 1541-1549 ◽  
Author(s):  
Li-Yeh Chuang ◽  
Yu-Huei Cheng ◽  
Cheng-Hong Yang
Keyword(s):  
Polymerase Chain Reaction ◽  
Primer Design ◽  
Specific Primer ◽  
Chain Reaction ◽  
Polymerase Chain

High performance Nanogold™-in situ hybridzation and its use in the detection of hybridized and PCR-amplified microscopical preparations

1996 ◽  
Vol 54 ◽  
pp. 896-897
Author(s):  
G. W. Hacker ◽  
I. Zehbe ◽  
J. Hainfeld ◽  
A.-H. Graf ◽  
C. Hauser-Kronberger ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Messenger Rna ◽  
High Performance ◽  
Detection System ◽  
Direct Methods ◽  
Genetic Alterations ◽  
Chain Reaction ◽  
Protein Encoding ◽  
Polymerase Chain

In situ hybridization (ISH) with biotin-labeled probes is increasingly used in histology, histopathology and molecular biology, to detect genetic nucleic acid sequences of interest, such as viruses, genetic alterations and peptide-/protein-encoding messenger RNA (mRNA). In situ polymerase chain reaction (PCR) (PCR in situ hybridization = PISH) and the new in situ self-sustained sequence replication-based amplification (3SR) method even allow the detection of single copies of DNA or RNA in cytological and histological material. However, there is a number of considerable problems with the in situ PCR methods available today: False positives due to mis-priming of DNA breakdown products contained in several types of cells causing non-specific incorporation of label in direct methods, and re-diffusion artefacts of amplicons into previously negative cells have been observed. To avoid these problems, super-sensitive ISH procedures can be used, and it is well known that the sensitivity and outcome of these methods partially depend on the detection system used.

1504: Molecular Diagnosis and Staging of Prostate Cancer Using Clusterin in Real Time Reverse Transcription Polymerase Chain Reaction (RT-PCR)

2006 ◽  
Vol 175 (4S) ◽  
pp. 485-486
Author(s):  
Sabarinath B. Nair ◽  
Christodoulos Pipinikas ◽  
Roger Kirby ◽  
Nick Carter ◽  
Christiane Fenske
Keyword(s):  
Prostate Cancer ◽  
Polymerase Chain Reaction ◽  
Real Time ◽  
Molecular Diagnosis ◽  
Reverse Transcription ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain
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