Inverted Terminal Repeats Permit the Average Length of Amplified DNA Fragments to Be Regulated during Preparation of cDNA Libraries by Polymerase Chain Reaction

1995 ◽  
Vol 229 (2) ◽  
pp. 198-202 ◽  
Author(s):  
K.A. Lukyanov ◽  
G.A. Launer ◽  
V.S. Tarabykin ◽  
A.G. Zaraisky ◽  
S.A. Lukyanov
Keyword(s):  
Polymerase Chain Reaction ◽  
Average Length ◽  
Cdna Libraries ◽  
Dna Fragments ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Inverted Terminal Repeats ◽  
Terminal Repeats

Plasma vs. serum in circulating tumor DNA measurement: characterization by DNA fragment sizing and digital droplet polymerase chain reaction

2020 ◽  
Vol 58 (4) ◽  
pp. 527-532 ◽  
Author(s):  
Jee-Soo Lee ◽  
Miyoung Kim ◽  
Moon-Woo Seong ◽  
Han-Sung Kim ◽  
Young Kyung Lee ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Circulating Tumor Dna ◽  
Analytical Sensitivity ◽  
Dna Fragments ◽  
Chain Reaction ◽  
Specimen Type ◽  
Dna Fragment ◽  
Polymerase Chain ◽  
Ctdna Analysis ◽  
Tumor Dna

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.

Direct Sequencing of DNA Fragments Amplified with Single Primers by Polymerase Chain Reaction without Cloning

1996 ◽  
Vol 241 (1) ◽  
pp. 136-139 ◽  
Author(s):  
Masayoshi Iizuka ◽  
Yuki Sugiyama ◽  
Shigeru Iida ◽  
Takao Sekiya
Keyword(s):  
Polymerase Chain Reaction ◽  
Direct Sequencing ◽  
Dna Fragments ◽  
Chain Reaction ◽  
Polymerase Chain

Variable stringency hybridization of polymerase chain reaction amplified HIV-1 DNA fragments

1990 ◽  
Vol 30 (2) ◽  
pp. 141-150 ◽  
Author(s):  
G. Agius ◽  
V. Kolesnitchenko ◽  
R. Snart ◽  
J.F. Zagury ◽  
K. Laaroubi ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Fragments ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Hiv 1

Detection of soluble methane monooxygenase producing Methylosinus trichosporium OB3b by polymerase chain reaction

1994 ◽  
Vol 40 (11) ◽  
pp. 969-973 ◽  
Author(s):  
K. S. Mohan ◽  
Satish K. Walia
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Methane Monooxygenase ◽  
Dna Fragments ◽  
Chain Reaction ◽  
Methylosinus Trichosporium Ob3b ◽  
Methylosinus Trichosporium ◽  
Soluble Methane Monooxygenase ◽  
Expected Length ◽  
Polymerase Chain

The soluble methane monooxygenase (sMMO) enzyme complex of methanotrophs cometabolizes haloaliphatic compounds such as trichloroethylene. Two 18-mer oligonucleotides as primary primers and a nested primer of the same length were selected to amplify specific DNA sequences of the sMMO gene cluster using polymerase chain reaction (PCR). Two DNA fragments of sizes 270 and 400 base pairs were obtained when purified DNA from the methanotroph Methylosinus trichosporium OB3b was used as template. The primers were specific for sMMO sequences of M. trichosporium, since none of the 13 bacterial isolates screened yielded the expected length of PCR-amplified DNA fragments. The detection limit of the PCR method was 5 × 102 cells of M. trichosporium. The sMMO sequences were successfully amplified in groundwater (containing native microbial population) when seeded with M. trichosporium, FP1 sense (5′-ATGTCCAGCGCTCATAAC-3′), RP1 antisense (5′-TCAGATGTCGGTCAGGGC-3′), FP2 sense nested (5′GCCATCATCGGTCAGGGC-3′), and FP2 sense nested (5′-GCCATCATCGAGGACATC-3′).Key words: detection, soluble methane monooxygenase, polymerase chain reaction, Methylosinus trichosporium OB3b.

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