TY - JOUR

T1 - pH-dependent binding of ATP aptamer to the target and competition strands: Fluorescent melting curve fitting study

AU - Gabrusenok, P.V.

AU - Ramazanov, R.R.

AU - Kasyanenko, N.A.

AU - Lantushenko, A.O.

AU - Sokolov, P.A.

N1 - Export Date: 19 October 2024 CODEN: BBGSB Адрес для корреспонденции: Sokolov, P.A.; St. Petersburg University, 13B Universitetskaya Emb., Russian Federation; эл. почта: p.a.sokolov@spbu.ru Химические вещества/CAS: adenosine triphosphate, 15237-44-2, 56-65-5, 987-65-5 Сведения о финансировании: Russian Science Foundation, RSF, 23–73-00130 Текст о финансировании 1: This study was supported by the Russian Science Foundation (project no. 23\u201373-00130).

PY - 2024/11/1

Y1 - 2024/11/1

N2 - The pH varies in different tissues and organelles and also changes during some diseases. In this regard, the application of molecular switches that use a competition-based aptamer switch design in biological systems requires studying the thermodynamics of such systems at different pH values. In this work, we studied the binding of the classical ATP aptamer to ATP and competition strands under different pH and ionic conditions using fluorescent melting curve analysis. We have developed an original approach to processing source data from a PCR thermal cycler. It is based on constructing a thermodynamic model of the melting profile and the subsequent fit of experimental curves within this model. We have shown that this approach enables us to narrow the temperature region under study to the width of the melting region without a significant loss in the quality of the result. This impressively expands the application area of this approach compared to frequently used techniques that require mandatory measurement of the signal outside the melting region. The results obtained by the method showed that the thermodynamic parameters of the ATP aptamer and its duplexes with competition strands change depending on pH. Therefore, molecular switches that use a competition strand to the ATP aptamer may have a pH-dependent sensitivity that has not been previously considered. This should be taken into account for future rational design of similar systems. © 2024 Elsevier B.V.

AB - The pH varies in different tissues and organelles and also changes during some diseases. In this regard, the application of molecular switches that use a competition-based aptamer switch design in biological systems requires studying the thermodynamics of such systems at different pH values. In this work, we studied the binding of the classical ATP aptamer to ATP and competition strands under different pH and ionic conditions using fluorescent melting curve analysis. We have developed an original approach to processing source data from a PCR thermal cycler. It is based on constructing a thermodynamic model of the melting profile and the subsequent fit of experimental curves within this model. We have shown that this approach enables us to narrow the temperature region under study to the width of the melting region without a significant loss in the quality of the result. This impressively expands the application area of this approach compared to frequently used techniques that require mandatory measurement of the signal outside the melting region. The results obtained by the method showed that the thermodynamic parameters of the ATP aptamer and its duplexes with competition strands change depending on pH. Therefore, molecular switches that use a competition strand to the ATP aptamer may have a pH-dependent sensitivity that has not been previously considered. This should be taken into account for future rational design of similar systems. © 2024 Elsevier B.V.

KW - Aptamer

KW - ATP

KW - Fluorescent

KW - Melting curve analysis

KW - Model

KW - Molecular switch

KW - pH

KW - Thermodynamics

KW - adenosine triphosphate

KW - aptamer

KW - fluorescent dye

KW - Article

KW - binding affinity

KW - curve fitting

KW - fluorescence

KW - fluorescent melting curve analysis

KW - ionization

KW - melting point

KW - molecular switch

KW - molecule

KW - process design

KW - thermodynamics

UR - https://www.mendeley.com/catalogue/03df0f24-8550-315f-bea7-6c1e9bf8363e/

U2 - 10.1016/j.bbagen.2024.130689

DO - 10.1016/j.bbagen.2024.130689

M3 - статья

VL - 1868

JO - Biochimica et Biophysica Acta - General Subjects

JF - Biochimica et Biophysica Acta - General Subjects

SN - 0006-3002

IS - 11

ER -