Influence of Nucleotide Context on Non-Specific Amplification of DNA with Bst exo DNA Polymerase.

Isothermal nucleic acids amplification that requires DNA polymerases with strand-displacement activity gained more attention in the last two decades. Among the DNA polymerases with strand-displacement activity, Bst exo is the most widely used. However, it tends to carry out nonspecific DNA synthesis through multimerization.

LAMPrimers iQ: New primer design software for loop-mediated isothermal amplification (LAMP).

Nucleic acids amplification is a widely used technique utilized for different manipulations with DNA and RNA. Although, polymerase chain reaction (PCR) remains the most popular amplification method, isothermal approaches are gained more attention last decades. Among these, loop-mediated isothermal amplification (LAMP) became an excellent alternative to PCR.

Detection of Specific RNA Targets by Multimerization.

Detection of specific RNA targets via amplification-mediated techniques is widely used in fundamental studies and medicine due to essential role of RNA in transfer of genetic information and development of diseases. Here, we report on an approach for detection of RNA targets based on the particular type of isothermal amplification, namely, reaction of nucleic acid multimerization. The proposed technique requires only a single DNA polymerase possessing reverse transcriptase, DNA-dependent DNA polymerase, and strand-displacement activities.

New method for microRNA detection based on multimerization.

Detection of specific microRNA (miRNA) is of great demand due to their essential role in genes regulation, stress response and development of diseases. However, mature miRNAs are small molecules that make it difficult to use routine amplification-based methods. Here, we report an approach for detection of miRNA based on a new type of isothermal amplification, namely, multimerization.

Reverse transcriptase-free detection of viral RNA using Hemo Klentaq DNA polymerase.

COVID-19 pandemic highlighted the demand for the fast and reliable detection of viral RNA. Although various methods for RNA amplification and detection have been proposed, some limitations, including those caused by reverse transcription (RT), need to be overcome. Here, we report on the direct detection of specific RNA by conventional polymerase chain reaction (PCR) requiring no prior RT step.

Encoding of non-biological information for its long-term storage in DNA.

In 2019, at the World Economic Forum, DNA data storage was indicated as one of the breakthroughs expected to radically impact the global socio-economic order. Indeed, dry DNA is a relatively stable substance and an extremely capacious information carrier. One gram of DNA can hold up to 455 exabytes, provided that one nucleotide encodes two bits of information.

Convective polymerase chain reaction in standard microtubes.

Polymerase chain reaction (PCR) is the most widely used method for nucleic acids amplification. To date, a huge number of versatile PCR techniques have been developed. One of the relevant goals is to shorten PCR duration, which can be achieved in several ways.

Inhibition of nonspecific polymerase activity using Poly(Aspartic) acid as a model anionic polyelectrolyte.

DNA polymerases with strand-displacement activity allow to amplify nucleic acids under isothermal conditions but often lead to undesirable by-products. Here, we report the increase of specificity of isothermal amplification in the presence of poly (aspartic) acids (pAsp). We hypothesized that side reactions occur due to the binding of the phosphate backbone of synthesized DNA strands with surface amino groups of the polymerase, and weakly acidic polyelectrolytes could shield polymerase molecules from DNA and thereby inhibit nonspecific amplification.

Data on molecular docking simulations of quaternary complexes 'Bst exo- polymerase-DNA-dCTP-metal cations'.

This article reports data related to the research article entitled "Effect of metal ions on isothermal amplification with Bst exo- DNA polymerase" (R.R. Garafutdinov, A.

A new digital approach to SNP encoding for DNA identification.

Identification of individuals has become an urgent problem for mankind. In the last three decades, STR-based DNA identification has actively evolved along with traditional biometric methods. Nonetheless, single-nucleotide polymorphisms (SNPs) are now of great interest and a number of relevant SNP panels have been proposed for DNA identification.

The influence of quality of primers on the formation of primer dimers in PCR.

Polymerase chain reaction (PCR) is the most commonly used method for nucleic acids amplification. PCR performance depends on several causes, among which the quality of primers is one of the main determinants affecting specificity, sensitivity and reliability of the reaction. Here, we report on the results of the detailed study devoted to the dimerization of the primers during PCR.

Effect of metal ions on isothermal amplification with Bst exo- DNA polymerase.

Over the last two decades, the isothermal amplification has become actively used for nucleic acids analysis. To perform isothermal techniques, DNA polymerases with strand-displacement activity are needed, and Bst exo- polymerase is one of the most widely used. However, Bst exo- is prone to non-specific DNA synthesis (e.

Enhancement of PCR efficiency using mono- and disaccharides.

Polymerase chain reaction is the most commonly used approach for nucleic acids amplification. Despite the variety of PCR methods have been proposed, new techniques are being developed to improve this reaction. We found that, in general, mono- and disaccharides can serve as effective PCR enhancers.

Data on multimerization efficiency for short linear DNA templates and phosphoryl guanidine primers during isothermal amplification with Bst exo- DNA polymerase.

This article reports experimental data related to the research article entitled "Prevention of DNA multimerization using phosphoryl guanidine primers during isothermal amplification with Bst exo- DNA polymerase" (R.R. Garafutdinov, A.

Prevention of DNA multimerization using phosphoryl guanidine primers during isothermal amplification with Bst exo- DNA polymerase.

Over the last two decades, isothermal amplification of nucleic acids has gained more attention due to a number of advantages over the widely used polymerase chain reaction. For isothermal amplification, DNA polymerases with strand-displacement activity are needed, and Bst exo- polymerase is one of the most commonly used. Unfortunately, Bst exo- causes nonspecific DNA amplification (so-called multimerization) under isothermal conditions that results in undesirable products (multimers) consisting of tandem nucleotide repeats.

The Influence of Reaction Conditions on DNA Multimerization During Isothermal Amplification with Bst exo- DNA Polymerase.

Methods for isothermal amplification of nucleic acids are gained more attention in the last two decades. For isothermal amplification, DNA polymerases with strand displacement activity are required, and Bst exo- is one of the most commonly used polymerases. However, Bst exo- is able to cause nonspecific DNA amplification through multimerization, which leads to a set of undesirable by-products.

The influence of CpG (5'-d(CpG)-3' dinucleotides) methylation on ultrasonic DNA fragmentation.

DNA methylation is an important way of gene regulation. The variety of methods for DNA methylation analysis based on chemical modification or enzyme digestion has been proposed. However, DNA is able to undergo transformations under physical power.

Polymerase chain reaction with nearby primers.

DNA analysis of biological specimens containing degraded nucleic acids such as mortal remains, archaeological artefacts, forensic samples etc. has gained more attention in recent years. DNA extracted from these samples is often inapplicable for conventional polymerase chain reaction (PCR), so for its amplification the nearby primers are commonly used.