scholarly journals Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification

2001 ◽  
Vol 11 (6) ◽  
pp. 1095-1099 ◽  
Author(s):  
F. B. Dean
Keyword(s):  
Dna Polymerase ◽  
Rolling Circle Amplification ◽  
Rolling Circle ◽  
Phi29 Dna Polymerase ◽  
Phage Dna ◽  
Rapid Amplification

scholarly journals In vitro evolution of phi29 DNA polymerases through compartmentalized gene expression and rolling-circle replication

2019 ◽  
Vol 32 (11) ◽  
pp. 481-487 ◽  
Author(s):  
Yoshihiro Sakatani ◽  
Ryo Mizuuchi ◽  
Norikazu Ichihashi
Keyword(s):  
Gene Expression ◽  
Dna Polymerase ◽  
Multiple Displacement Amplification ◽  
Rolling Circle Amplification ◽  
Expression System ◽  
Rolling Circle Replication ◽  
Rolling Circle ◽  
Dna Labeling ◽  
Phi29 Dna Polymerase

Abstract Phi29 DNA polymerase is widely used for DNA amplification through rolling-circle replication or multiple displacement amplification. Here, we performed completely in vitro artificial evolution of phi29 DNA polymerase by combining the in vitro compartmentalization and the gene expression-coupled rolling-circle replication of a circular DNA encoding the polymerase. We conducted the experiments in six different conditions composed of three different levels of inhibitor concentrations with two different DNA labeling methods. One of the experiments was performed in our previous study and the other five experiments were newly conducted in this study. Under all conditions, we found several mutations that enhance the rolling-circle amplification by the polymerase when it was expressed in the reconstituted gene expression system. Especially, a combinatorial mutant polymerase (K555T/D570N) exhibits significantly higher rolling-circle activity than the wild type. These highly active mutant polymerases would be useful for various applications.

Wide diversity of PAX5 alterations in B-ALL: a Groupe Francophone de Cytogénétique Hématologique study

Blood ◽  
2010 ◽  
Vol 115 (15) ◽  
pp. 3089-3097 ◽  
Author(s):  
Etienne Coyaud ◽  
Stephanie Struski ◽  
Nais Prade ◽  
Julien Familiades ◽  
Ruth Eichner ◽  
...  
Keyword(s):  
Lymphoblastic Leukemia ◽  
Rolling Circle Amplification ◽  
High Variability ◽  
Comparative Genomic ◽  
Fusion Genes ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Rolling Circle ◽  
Rapid Amplification ◽  
Innovative Techniques

Abstract PAX5 is the main target of somatic mutations in acute B lymphoblastic leukemia (B-ALL). We analyzed 153 adult and child B-ALL harboring karyotypic abnormalities at chromosome 9p, to determine the frequency and the nature of PAX5 alterations. We found PAX5 internal rearrangements in 21% of the cases. To isolate fusion partners, we used classic and innovative techniques (rolling circle amplification-rapid amplification of cDNA ends) and single nucleotide polymorphism-comparative genomic hybridization arrays. Recurrent and novel fusion partners were identified, including NCoR1, DACH2, GOLGA6, and TAOK1 genes showing the high variability of the partners. We noted that half the fusion genes can give rise to truncated PAX5 proteins. Furthermore, malignant cells carrying PAX5 fusion genes displayed a simple karyotype. These data strongly suggest that PAX5 fusion genes are early players in leukemogenesis. In addition, PAX5 deletion was observed in 60% of B-ALL with 9p alterations. Contrary to cases with PAX5 fusions, deletions were associated with complex karyotypes and common recurrent translocations. This supports the hypothesis of the secondary nature of the deletion. Our data shed more light on the high variability of PAX5 alterations in B-ALL. Therefore, it is probable that gene fusions occur early, whereas deletions should be regarded as a late/secondary event.

scholarly journals TempliPhi, ⌽29 DNA Polymerase Based Rolling Circle Amplification of Templates for DNA Sequencing

BioTechniques ◽  
2002 ◽  
Vol 32 (6S) ◽  
pp. S44-S47 ◽  
Author(s):  
John R. Nelson ◽  
Yuyang Christine Cai ◽  
Theresa L. Giesler ◽  
Joseph W. Farchaus ◽  
Shanmuuga T. Sundaram ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Dna Polymerase ◽  
Rolling Circle Amplification ◽  
Rolling Circle

Amplification of Padlock Probes for DNA Diagnostics by Cascade Rolling Circle Amplification or the Polymerase Chain Reaction

1999 ◽  
Vol 123 (12) ◽  
pp. 1170-1176 ◽  
Author(s):  
David C. Thomas ◽  
Glenn A. Nardone ◽  
Sandra K. Randall
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Polymerase ◽  
Rolling Circle Amplification ◽  
Strand Displacement ◽  
Chain Reaction ◽  
Dna Diagnostics ◽  
Gene Target ◽  
Rolling Circle ◽  
Padlock Probes ◽  
Polymerase Chain

Abstract Context.—Padlock probes are highly specific reagents for DNA diagnostics that can discriminate gene sequences with single base mutations. When the 3′ and 5′ terminal regions of the oligonucleotide probes are juxtaposed on a target DNA sequence, they can be circularized by enzymatic ligation and become topologically locked to the target. However, to be useful in solution-based diagnostics, the sensitivity of padlock probes must be markedly enhanced. Objective.—To describe two methods for geometric amplification of circularized padlock probes. Design.—Cascade rolling circle amplification is an isothermal system that uses generic primers and a DNA polymerase with strong strand displacement activity to amplify circularized probes by a mechanism combining rolling circle replication and strand displacement synthesis. One of the primers was designed as an energy transfer–labeled primer, which generates a fluorescence signal only when incorporated into the amplified product, enabling a direct means of detection. Results.—Using pUC19 as a model target to circularize an 89-base probe, a 10 billion–fold amplification was achieved with Bst DNA polymerase (large fragment) within 1 hour starting with as few as 10 probe molecules. The polymerase chain reaction was also used to amplify ligated padlock probes in a rare target detection system. In mixing experiments containing both normal and mutant p53 or c-Ki-ras2 gene target sequences, mutant targets were easily detected in the presence of a 500-fold excess of normal target copies. Conclusion.—These results indicate that padlock probes can be amplified to the high levels required for solution-based DNA diagnostics.

Rolling Circle Amplification of Cyclizable Dna Probes by ∅29 Dna Polymerase: A Tool for in Situ Single-Copy Gene Detection.

1997 ◽  
Vol 3 (S2) ◽  
pp. 201-202
Author(s):  
Paul M. Lizardi ◽  
Patricia Bray-Ward ◽  
David C. Ward
Keyword(s):  
Dna Polymerase ◽  
Rolling Circle Amplification ◽  
Single Copy ◽  
Rolling Circle Replication ◽  
Gene Detection ◽  
Rolling Circle ◽  
Padlock Probes ◽  
Cytological Localization ◽  
High Degree

Oligonucleotide probes that can be cyclized by ligation (“padlock probes”) provide a very high degree of recognition specificity. Nilsson et al. have demonstrated the used of padlock probes for the cytological localization of alphoid repeats in chromosome 12. We have been extending the use of padlock probes to the detection of single copy sequences, and with this in mind have explored the amplification of DNA circles.We designed a primer complementary to the arbitrary backbone (non-probing) sequence of a 92-base closed circular probe oligonucleotide and investigated the kinetics of rolling circle replication. Using the highly processive, strand-displacing DNA polymerase of phage ∅29 (kindly provided by Dr. Margarita Salas, CSIC, Madrid, Spain) we demonstrated that several hundred tandem copies of the circular oligonucleotide are generated in a few minutes of incubation at 32°C. Because the amplified DNA remains hybridized to the circle in a rolling circle reaction, this method of amplification offers unique advantages for in situ gene detection since the amplified DNA can not diffuse away from the site of synthesis.

scholarly journals Engineered viral DNA polymerase with enhanced DNA amplification capacity: a proof-of-concept of isothermal amplification of damaged DNA

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Carlos D. Ordóñez ◽  
Ana Lechuga ◽  
Margarita Salas ◽  
Modesto Redrejo-Rodríguez
Keyword(s):  
Dna Polymerase ◽  
Rolling Circle Amplification ◽  
Dna Amplification ◽  
Proof Of Concept ◽  
Abasic Site ◽  
Binding Motifs ◽  
Rolling Circle ◽  
Dna Binding Motifs ◽  
Dramatic Growth ◽  
Damaged Dna

Abstract The development of whole genome amplification (WGA) and related methods, coupled with the dramatic growth of sequencing capacities, has changed the paradigm of genomic and genetic analyses. This has led to a continual requirement of improved DNA amplification protocols and the elaboration of new tailored methods. As key elements in WGA, identification and engineering of novel, faithful and processive DNA polymerases is a driving force in the field. We have engineered the B-family DNA polymerase of virus Bam35 with a C-terminal fusion of DNA-binding motifs. The new protein, named B35-HhH, shows faithful DNA replication in the presence of magnesium or an optimised combination of magnesium and manganese divalent cofactors, which enhances the replication of damaged DNA substrates. Overall, the newly generated variant displays improved amplification performance, sensitivity, translesion synthesis and resistance to salt, which are of great interest for several applications of isothermal DNA amplification. Further, rolling-circle amplification of abasic site-containing minicircles provides a proof-of-concept for using B35-HhH for processive amplification of damaged DNA samples.

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