Journal Article

Modeling a Standard Loop-Mediated Isothermal Amplification Reaction and Its Modification Involving Additional Inner Primers

Mikhaylenko, Constantin I., Gubaydullin, Irek M., Akhmetzianova, Liana U., Chemeris, Alexey V., Sakhabutdinova, Assol R., Garafutdinov, Ravil R., Chemeris, Dmitry A., Khairitdinov, Valery D.

2025

Overview

Loop-mediated isothermal amplification (LAMP) was developed a quarter of a century ago, but it is still not exactly clear how this reaction proceeds. Only a few articles have focused on the kinetics of LAMP and the types of products formed. In this work, 10 types were identified and named. A basic dumbbell structure, Z6_dmb(1), consists of six zones and triggers the LAMP cycle. Due to self-priming, Z6_dmb(1) transforms into hairpin structure Z9_hp(1) and then into linearized strand Z9_li(1), carrying also strand Z6_dmb(2). Through similar transformations, it again generates strand Z6_dmb(1), completing the first LAMP cycle and starting a new one. The next stage of the exponential phase starts from two Z15_hp hairpin structures generated in the LAMP cycle, which next turn into Z15_li → Z27_hp → Z27_li → Z51_hp → and so forth. Modeling of a new type of the reaction, namely, pseudo-hemi-nested LAMP (phn-LAMP), was carried out. phn-LAMP involves three inner primers: two forward (FIP and extraFIP) and one backward inner primer, or vice versa. phn-LAMP has an advantage over LAMP involving loop or stem primers and over MIP-LAMP (multiple inner primers).

• Publisher: MDPI AG,MDPI
• Subject: Chemical properties / Comparative analysis / Coronaviruses / DNA Primers - chemistry / DNA Primers - genetics / Enzymes / Gene amplification / LAMP nomenclature / lamplicons / loop-mediated isothermal amplification (LAMP) / Mathematical models / Molecular Diagnostic Techniques / Nucleic Acid Amplification Techniques - methods / Nucleic Acid Conformation / Physiological aspects / primer design / Primers / pseudo-hemi-nested LAMP (phn-LAMP)