scholarly journals A strong strand displacement activity of thermostable DNA polymerase markedly improves the results of DNA amplification

BioTechniques ◽  
2014 ◽  
Vol 57 (2) ◽  
Author(s):  
Konstantin B. Ignatov ◽  
Ekaterina V. Barsova ◽  
Arkady F. Fradkov ◽  
Konstantin A. Blagodatskikh ◽  
Tatiana V. Kramarova ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Dna Amplification ◽  
Strand Displacement ◽  
Displacement Activity ◽  
Thermostable Dna Polymerase

scholarly journals Capacity of Nine Thermostable DNA Polymerases To Mediate DNA Amplification in the Presence of PCR-Inhibiting Samples

1998 ◽  
Vol 64 (10) ◽  
pp. 3748-3753 ◽  
Author(s):  
Waleed Abu Al-Soud ◽  
Peter Rådström
Keyword(s):  
Dna Polymerase ◽  
Biological Samples ◽  
Detection Method ◽  
Dna Polymerases ◽  
Dna Amplification ◽  
Nucleic Acid Amplification ◽  
Full Potential ◽  
Thermus Aquaticus ◽  
Pcr Inhibitors ◽  
Thermostable Dna Polymerase

ABSTRACT The PCR is an extremely powerful method for detecting microorganisms. However, its full potential as a rapid detection method is limited by the inhibition of the thermostable DNA polymerase fromThermus aquaticus by many components found in complex biological samples. In this study, we have compared the effects of known PCR-inhibiting samples on nine thermostable DNA polymerases. Samples of blood, cheese, feces, and meat, as well as various ions, were added to PCR mixtures containing various thermostable DNA polymerases. The nucleic acid amplification capacity of the nine polymerases, under buffer conditions recommended by the manufacturers, was evaluated by using a PCR-based detection method for Listeria monocytogenes in the presence of purified template DNA and different concentrations of PCR inhibitors. The AmpliTaqGold and the Taq DNA polymerases from Thermus aquaticus were totally inhibited in the presence of 0.004% (vol/vol) blood in the PCR mixture, while the HotTub, Pwo, rTth, andTfl DNA polymerases were able to amplify DNA in the presence of 20% (vol/vol) blood without reduced amplification sensitivity. The DNA polymerase from Thermotoga maritima(Ultma) was found to be the most susceptible to PCR inhibitors present in cheese, feces, and meat samples. When the inhibitory effect of K and Na ions was tested on the nine polymerases, HotTub from Thermus flavus and rTthfrom Thermus thermophilus were the most resistant. Thus, the PCR-inhibiting effect of various components in biological samples can, to some extent, be eliminated by the use of the appropriate thermostable DNA polymerase.

scholarly journals Strand Displacement Activity of PrimPol

2020 ◽  
Vol 21 (23) ◽  
pp. 9027
Author(s):  
Elizaveta O. Boldinova ◽  
Ekaterina A. Belousova ◽  
Diana I. Gagarinskaya ◽  
Ekaterina A. Maltseva ◽  
Svetlana N. Khodyreva ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Strand Displacement ◽  
Displacement Activity

Human PrimPol is a unique enzyme possessing DNA/RNA primase and DNA polymerase activities. In this work, we demonstrated that PrimPol efficiently fills a 5-nt gap and possesses the conditional strand displacement activity stimulated by Mn2+ ions and accessory replicative proteins RPA and PolDIP2. The DNA displacement activity of PrimPol was found to be more efficient than the RNA displacement activity and FEN1 processed the 5′-DNA flaps generated by PrimPol in vitro.

scholarly journals 3′ to 5′ Exonuclease Activity of Herpes Simplex Virus Type 1 DNA Polymerase Modulates Its Strand Displacement Activity

2003 ◽  
Vol 77 (18) ◽  
pp. 10147-10153 ◽  
Author(s):  
Yali Zhu ◽  
Kelly S. Trego ◽  
Liping Song ◽  
Deborah S. Parris
Keyword(s):  
Herpes Simplex Virus ◽  
Herpes Simplex ◽  
Dna Polymerase ◽  
Virus Type ◽  
Herpes Simplex Virus Type ◽  
Strand Displacement ◽  
Displacement Activity ◽  
Simplex Virus ◽  
Hsv 1

ABSTRACT Using a minicircle DNA primer-template, the wild-type catalytic subunit of herpes simplex virus type 1 (HSV-1) DNA polymerase (pol) was shown to lack significant strand displacement activity with or without its processivity factor, UL42. However, an exonuclease-deficient (exo−) pol (D368A) was capable of slow strand displacement. Although UL42 increased the rate (2/s) and processivity of strand displacement by exo− pol, the rate was slower than that for gap-filling synthesis. High inherent excision rates on matched primer-templates and rapid idling-turnover (successive rounds of excision and polymerization) of exo-proficient polymerases correlated with poor strand displacement activity. The results suggest that the exo activity of HSV-1 pol modulates its ability to engage in strand displacement, a function that may be important to the viability and genome stability of the virus.

Nanoporous scaffold for DNA polymerase: pore-size optimisation of mesoporous silica for DNA amplification

RSC Advances ◽  
2014 ◽  
Vol 4 (49) ◽  
pp. 25920-25923 ◽  
Author(s):  
Shun-ichi Matsuura ◽  
Tomoya Baba ◽  
Manami Chiba ◽  
Tatsuo Tsunoda
Keyword(s):  
Mesoporous Silica ◽  
Pore Size ◽  
Dna Polymerase ◽  
Dna Amplification ◽  
Mesoporous Silicas ◽  
Size Regulation ◽  
Thermostable Dna Polymerase

The simple and selective immobilisation of a thermostable DNA polymerase on mesoporous silicas was achieved, and DNA amplification activity was retained under the pore-size regulation of the mesoporous silicas.

scholarly journals Pif1 removes a Rap1-dependent barrier to the strand displacement activity of DNA polymerase δ

2016 ◽  
Vol 44 (8) ◽  
pp. 3811-3819 ◽  
Author(s):  
Katrina N. Koc ◽  
Saurabh P. Singh ◽  
Joseph L. Stodola ◽  
Peter M. Burgers ◽  
Roberto Galletto
Keyword(s):  
Dna Polymerase ◽  
Strand Displacement ◽  
Displacement Activity ◽  
Dna Polymerase Δ

scholarly journals DNA-directed DNA Polymerase and Strand Displacement Activity of the Reverse Transcriptase Encoded by the R2 Retrotransposon

2007 ◽  
Vol 374 (2) ◽  
pp. 322-333 ◽  
Author(s):  
Anna Kurzynska-Kokorniak ◽  
Varuni K. Jamburuthugoda ◽  
Arkadiusz Bibillo ◽  
Thomas H. Eickbush
Keyword(s):  
Reverse Transcriptase ◽  
Dna Polymerase ◽  
Strand Displacement ◽  
Displacement Activity

Amplification of RNA: High-Temperature Reverse Transcription and DNA Amplification with a Magnesium-Activated Thermostable DNA Polymerase

2006 ◽  
Vol 2006 (1) ◽  
pp. pdb.prot4115
Author(s):  
Edward S. Smith ◽  
Alvin K. Li ◽  
Alice M. Wang ◽  
David H. Gelfand ◽  
Thomas W. Myers
Keyword(s):  
High Temperature ◽  
Dna Polymerase ◽  
Reverse Transcription ◽  
Dna Amplification ◽  
Thermostable Dna Polymerase
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