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

Akhmetzianova, Liana U.; Davletkulov, Timur M.; Sakhabutdinova, Assol R.; Chemeris, Alexey V.; Gubaydullin, Irek M.; Garafutdinov, Ravil R.

doi:10.1016/j.ab.2023.115376

Cited by 3 publications

(3 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The primer design of the LAMP reaction is complex, requiring 4–6 primers in the reaction system. In order to solve this problem, researchers have developed the software or the website for designing LAMP primers, which has greatly reduced the difficulty of designing LAMP primers, making the LAMP reaction more widely used [ 12 ]. In general, LAMP amplification, as one of the most widely used isothermal amplification methods, has the following advantages: (1) The reaction temperature is around 65 °C and does not require a pre-heating step.…”

Section: Introductionmentioning

confidence: 99%

A Point-of-Care Nucleic Acid Quantification Method by Counting Light Spots Formed by LAMP Amplicons on a Paper Membrane

Chen,

Zhu,

Peng

et al. 2024

Biosensors

View full text Add to dashboard Cite

Nucleic acid quantification, allowing us to accurately know the copy number of target nucleic acids, is significant for diagnosis, food safety, agricultural production, and environmental protection. However, current digital quantification methods require expensive instruments or complicated microfluidic chips, making it difficult to popularize in the point-of-care detection. Paper is an inexpensive and readily available material. In this study, we propose a simple and cost-effective paper membrane-based digital loop-mediated isothermal amplification (LAMP) method for nucleic acid quantification. In the presence of DNA fluorescence dyes, the high background signals will cover up the amplicons-formed bright spots. To reduce the background fluorescence signals, a quencher-fluorophore duplex was introduced in LAMP primers to replace non-specific fluorescence dyes. After that, the amplicons-formed spots on the paper membrane can be observed; thus, the target DNA can be quantified by counting the spots. Take Vibrio parahaemolyticus DNA detection as an instance, a good linear relationship is obtained between the light spots and the copy numbers of DNA. The paper membrane-based digital LAMP detection can detect 100 copies target DNA per reaction within 30 min. Overall, the proposed nucleic acid quantification method has the advantages of a simple workflow, short sample-in and answer-out time, low cost, and high signal-to-noise, which is promising for application in resourced limited areas.

show abstract

Section: Introductionmentioning

confidence: 99%

A Point-of-Care Nucleic Acid Quantification Method by Counting Light Spots Formed by LAMP Amplicons on a Paper Membrane

Chen,

Zhu,

Peng

et al. 2024

Biosensors

View full text Add to dashboard Cite

show abstract

“…First, primer panels for LAMP assays are more difficult to design than PCR and qPCR assays, since the primer set solution space is constrained by additional thermodynamic, length, and distance requirements. Several software applications, like the NEB® LAMP Primer Design Tool or Primer Explorer, can help design primers based on user-input target sequences, but these applications do not provide specificity metrics for the resulting assay with respect to taxonomy (13)(14)(15). Second, once a successful assay panel has been designed, the resulting colorimetric change must be assessed visually for the presence or absence of the pathogen.…”

Section: Introductionmentioning

confidence: 99%

Loop-Mediated Isothermal Amplification Assays for the Detection of Antimicrobial Resistance Elements inVibrio cholerae

Negrón,

Trivedi,

Tolli

et al. 2024

Preprint

View full text Add to dashboard Cite

The bacteriumVibrio choleraecauses diarrheal illness and can acquire genetic material leading to multiple drug resistance (MDR). Rapid detection of resistance-conferring mobile genetic elements helps avoid the prescription of ineffective antibiotics. Colorimetric loop-mediated isothermal amplification (LAMP) assays provide a rapid and cost-effective means for detection at point-of-care, but it can be difficult to design primer sets, determine target specificity, and interpret subjective color changes. We developed an algorithm for thein silicodesign and evaluation of LAMP assays within the open-source PCR Signature Erosion Tool (PSET) and a computer vision application for the quantitative analysis of colorimetric outputs. As an example, we generated new LAMP assays targeting drug resistance inV. choleraeand evaluated existing ones based onin silicotarget specificity andin vitrotesting. Improvements in the design and testing of LAMP assays, with heightened target specificity and a simple analysis platform, increase utility for in-field applications.

show abstract

“…Рис. 1 Схематичное расположение мест отжига внешних и внутренних праймеров для LAMP-амплификации [6] Позже теми же авторами был предложен модифицированный метод, предлагающий использование не четырех, а шести праймеров, отжигающихся уже на восьми участках целевой нуклеотидной последовательности [7]. Предлагалось добавить еще два петлевых праймера (Loop B, Loop F), которые должны вступить в реакцию на третьем этапе после образования гантелеобразной структуры ДНК и отжигаться между участками F1/F2 и B1/B2 соответственно.…”

unclassified

Computer Program for Primer Design for Loop-Mediated Isothermal Amplification (LAMP)

Akhmetzianov

2024

Vestnik Donskogo gosudarstvennogo tehničeskogo universiteta

View full text Add to dashboard Cite

Introduction. To date, numerous methods of nucleic acid amplification have been proposed, and each method has a number of advantages and disadvantages. One of the most popular methods is Loop-mediated isothermal AMPlification (LAMP). Unlike thermocyclic reactions, such as PCR (polymerase chain reaction), which require three temperature changes and expensive equipment, in LAMP, the entire reaction takes place at one and the same temperature and at the maximum rate possible. An important component of LAMP-amplification is primers (usually 20–25 nucleotides), which need to be matched to a specific part of the nucleotide sequence. It is known that DNA sequence contains four nucleotides: A — adenine and T — thymine, G — guanine and C — cytosine. There is a huge variety of permutations of these nucleotides, and it is practically impossible to analyze such a large amount of data manually. Therefore, there is a need to use modern computer technologies. More than 150 computer programs have been proposed for the design of PCR primers, while for LAMP-primers there are less than 10 of them, and each of them has a number of drawbacks, e.g., in terms of the length of the analyzed site. Therefore, this work is aimed at developing a new domestic computer program for the design of specific primers for LAMP.Materials and Methods. The primer search algorithm was based on a linear search for a substring in a string, taking into account the criteria of primer selection for LAMP. The program complex of LAMP-primer design was implemented in Python programming language. The bioPython library was used to work with various DNA and RNA, and the Qt framework was used to develop the interface.Results. A modification of the direct sampling method using a stencil approach was proposed, taking into account the GC composition and annealing temperature of primers depending on their structure. A software package with a friendly interface was developed. It took into account the design criteria of primers: certificates of registration of computer programs (LAMPrimers iQ No. 2022617417 dated April 20, 2022, LAMPrimers iQ_loop No. 2023662840 dated June 14, 2023) were received. The program is in the public domain at https://github.com/Restily/LAMPrimers-iQDiscussion and Conclusion. The developed software packages can be used for research and analysis in molecular biology and genetics, to create diagnostic test systems that provide high sensitivity and reliability of detection of specific DNA and RNA. The software packages can be used in research institutes and laboratories engaged in the amplification of nucleic acids. The results of evaluating the selected sets of primers for the LAMP reaction were tested, and the effectiveness of working sets using the LAMPrimers iQ program was experimentally proven by the example of the detection of genetic material of the SARS-CoV-2 coronavirus.

show abstract

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

Cited by 3 publications

References 32 publications

A Point-of-Care Nucleic Acid Quantification Method by Counting Light Spots Formed by LAMP Amplicons on a Paper Membrane

A Point-of-Care Nucleic Acid Quantification Method by Counting Light Spots Formed by LAMP Amplicons on a Paper Membrane

Loop-Mediated Isothermal Amplification Assays for the Detection of Antimicrobial Resistance Elements inVibrio cholerae

Computer Program for Primer Design for Loop-Mediated Isothermal Amplification (LAMP)

Contact Info

Product

Resources

About