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7. Peptide Regulation of Gene Expression and Protein Synthesis in Bronchial Epithelium

Author

Khavinson, V. Kh., Tendler, S. M., Vanyushin, B. F., Kasyanenko, N. A., Kvetnoy, I. M., Linkova, N. S., Ashapkin, V. V., Polyakova, V. O., Basharina, V. S., and Bernadotte, A.

Subjects
Gene expression -- Research, Bronchitis -- Research -- Risk factors -- Genetic aspects -- Care and treatment, Protein synthesis -- Research, Health
Abstract

Introduction Some studies have shown that peptides have high treatment potential due to their biological activity, harmlessness, and tissue-specific action. Tetrapeptide Ala-Asp-Glu-Leu (ADEL) was effective on models of acute bacterial lung inflammation, fibrosis, and toxic lung damage in several studies. Methods We measured Ki67, Mcl-1, p53, CD79, and NOS-3 protein levels in the 1st, 7th, and 14th passages of bronchoepithelial human embryonic cell cultures. Gene expression of NKX2-1, SCGB1A1, SCGB3A2, FOXA1, FOXA2, MUC4, MUC5AC, and SFTPA1 was measured by real-time polymerase chain reaction. Using the methods of spectrophotometry, viscometry, and circular dichroism, we studied the ADEL-DNA interaction in vitro. Results Peptide ADEL regulates the levels of Ki67, Mcl-1, p53, CD79, and NOS-3 proteins in cell cultures of human bronchial epithelium in various passages. The strongest activating effect of peptide ADEL on bronchial epithelial cell proliferation through Ki67 and Mcl-1 was observed in 'old' cell cultures. ADEL regulates the expression of genes involved in bronchial epithelium differentiation: NKX2-1, SCGB1A1, SCGB3A2, FOXA1, and FOXA2. ADEL also activates several genes, which reduced expression correlated with pathological lung development: MUC4, MUC5AC, and SFTPA1. Spectrophotometry, viscometry, and circular dichroism showed ADEL-DNA interaction, with a binding region in the major groove (N7 guanine). Conclusions ADEL can bind to specific DNA regions and regulate gene expression and synthesis of proteins involved in the differentiation and maintenance of functional activity of the bronchial epithelium. Through activation of some specific gene expression, peptide ADEL may protect the bronchial epithelium from pulmonary pathology. ADEL also may have a geroprotective effect on bronchial tissue., Author(s): V. Kh. Khavinson[sup.2] [sup.5] , S. M. Tendler[sup.1] [sup.5] , B. F. Vanyushin[sup.3] , N. A. Kasyanenko[sup.4] , I. M. Kvetnoy[sup.5] [sup.6] , N. S. Linkova[sup.5] , V. V. [...]

Published
2014
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17. Contributory presentations/posters

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Gries, A., Singh, Balwinder, Nakazawal, Chicko, Genest, D., Getzoff, E. D., Matsuo, H., Kaur, Harpreet, Borst, J. W., Chadha, K. C., Tingyun, Kuang, Jagannadham, M. V., Leijon, Mikael, Sato, S., Bhakuni, Vlnod, Vijayan, M., Surolia, A., Suguna, K., Manoj, N., Srinivas, V. R., Ravishankar, R., Laggner, P., Prassl, R., Schwarzenbacher, R., Zeth, K., Kostner, G. M., Taylor, Susan S., Xuong, Nguyen-huu, Akamine, Pearl, Sagar, Bidva M., Saikrishnan, K., Purnapatre, K., Handa, P., Roy, S., Varshney, U., Biswal, B. K., Sukumar, N., Rao, J. K. Mohana, Johnson, A., Pattabhi, Vasantha, Murthy, M. R. N., Krishna, Sri S., Savithri, H. S., Sastri, Mira, Hosur, M. V., Pillai, Bindu, Kannan, K. K., Kumar, Mukesh, Patwardhan, Swati, Padmanabhaa, B., Sasaki-Sugio, S., Matsuzaki, T., Nukaga, M., Singh, T. P., Sharma, A. K., Srinivasan, A., Khan, J. A., Paramasivam, M., Kumar, P., Karthikevan, S., Sharma, S., Yadav, S., Srintvasan, A., Alam, Neelima, Gourinath, S., Kaur, Punit, Chandra, Vikas, Betzel, Ch., Ghosh, S., Bera, A. K., Pal, A. K., Baneriee, Asok, Mukhopadhyay, B. P., Bhattacharya, S., Chakraborty, S., Haldar, U., Dey, I., Solovicova, Adriana, Sevcik, Jozef, Sekar, K., Sundaralingam, M., Genov, N., Liang, Dong-cai, Zhang, Ji-ping, Jiang, Tao, Chang, Wen-rui, Blommers, Marcel, Jahnke, Wolfgang, Hosur, R. V., Panchal, S. C., Pillay, Bindu, Jaganathan, N. R., Mathur, Puniti, Srivatsun, S., Joshi, Ratan Mani, Chauhan, V. S., Govil, Girjesh, Atreya, H. S., Sahu, S. C., Quinjou, Éric, Adjadj, Elisabeth, Mispelter, Joël, Izadi-Pruneyre, Nadia, Blouquit, Yves, Heyd, Bernadette, Lerat, Guilhem, Desmadreil, Michel, Milnard, Philippe, Lin, Y., Rao, B. D. 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H., Jazbinšek, V., Tronteli, Z., Thiel, G., Wübeller, G., Müller, W., Brumen, Milan, Fajmut, Leš, Marhl, Marko, Volotovski, I. D., Sokolovski, S. G., Knight, M. R., Chalyi, Alexander V., Vasilʼev, Alexei N., Sharma, P., Pant, H. C., Sharma, M., Amin, N. D., Albers, R. W., Steinbach, P. J., Barchir, J., Balasubramanyam, M., Gardner, J. P., Condrescu, M., Pilarczyk, Gotz, Greulich, K. O., Monajembashi, Shamci, El-Awadi, A. I., El-Refaei, F. M., Talaat, M. M., Ali, F. M., Zahradniková, Alexandra, Tahradník, Ivan, Pavelková, Jana, Zhorov, Boris S., Ananthanaravanan, Vettai S., Weiss, D. G., Martin, D., Gornik, E., Neu, E., Michailov, Ch. M., Welscher, U., Seidenbusch, W., Jellali, A., Pattnaik, B. R., Hicks, D., Dreyfus, H., Sahel, J., Picaud, S., Forster, V., Wang, Hong-Wei, Sui, Sen-fang, Luther, Pradeep K., Morris, Ed, Barry, John, Squire, John, Sundari, Sivakama C., Balasubramanian, D., Christlet, Hema Thanka T., Veluraia, K., Suresh, Xavier M., Laretta-Garde, V., Krilov, Dubravka, Herak, Janko N., Stojanović, Nataša, Ferrone, Frank A., Ivanova, Maria, Jasuja, Ravi, Mirchev, Rossen, Stopar, David, Wolfs, Cor J. A. M., Hemminga, Marcus A., Spruijt, Ruud B., Arcovito, G., De Spirito, M., Frank, Joachim, Heagle, Amy B., Grassucci, Robert, Penczek, Pawel, Agrawal, Rajendra K., Sharma, Manjuli R., Wagenknecht, Terence, Jeyakumar, Loice H., Fleischer, Sidney, Knupp, Carlo, Squire, John M., Ezra, Eric, Munro, Peter M. G., Kitazawa, Hidefumi, Ichihara, Koji, Itoh, Tomohiko J., Iguchi, Yusuke, Pifat, Greta, Kveder, Marina, Pečar, Slavko, Schara, Milan, Nair, Deepak, Singh, Kavita, Rao, Kanury V. S., Sundaravadivel, B., Jain, Deepti, Kaur, Kanwaljeet, Salunke, D. M., Goel, Manisha, Kovalenko, E. I., Semenkova, G. N., Cherenkevich, S. N., Loganathan, D., Lakshmanan, T., Sriram, D., Srinivasan, S., Lebrón, J. A., Bjorkman, P. J., Ramalingam, T. S., Singh, A. K., Gayatri, T. N., Bisch, Paulo M., Caffarena, Ernesto R., Grigera, Raul J., Fromherz, P., Kiessling, V., Suresh, C. G., Rao, K. N., Khan, M. I., Gaikwad, S. M., Elanthiraiyan, M., Kaliannan, P., Payne, J., Chadha, K., Ambrus, J. L., Nair, M. P. N., Nair, Madhavan P. N., Hewitt, R., Schwartz, S. A., Mahajan, S., Macherel, D., Bourguignon, J., Neuburger, M., Douce, R., Cohen-Addad, C., Faure, M., Ober, R., Sieker, L., Gurumurthy, D. S., Velmurugan, S., Lobo, Z., Phadke, Ratna S., Desai, Prashant, Alieva, D. R., Guseinova, I. M., Zulfugarov, I. S., Aliev, J. A., Ismayilov, M. A., Novruzova, S. N., Savchenko, T. V., Suleimanov, Yu. S., Bartošková, Hana, Nauš, Jan, Ilík, Petr, Kouřil, Roman, Vidyasagar, P. B., Thomas, Sarah, Gaikwad, Jvoti U., Cseh, Z., Mustárdy, L., Garab, G., Simidjiev, I., Rajagopal, S., Várkonyi, Zs., Holzenburg, A., Stoylova, S., Papp, E., Millar, D. P., Bruder, R., Woo, T. T., Genick, U. K., Gerwert, K., Jávorfí, Tamás, Garab, Győző, Naqvi, Razi K., Gaikwad, Jyoti, Kalimullah, Md., Semwal, Manoj, Naus, Man, Ilik, Petr, Kouril, Roman, Horváth, Gábor, Bernard, Gary D., Pomozi, István, Wehner, Rüdiger, Damjanović, Ana, Schulten, Klaus, Ritz, Thorsten, Yandao, Gong, Jushuo, Wang, Nanming, Zhao, Jixiu, Shan, Freiberg, Arvi, Timpmann, Kõu, Woodbury, Neal W., Ruus, Rein, Nemtseva, E. V., Kudryasheva, N. S., Sizykh, A. G., Tikhomirov, A. A., Nesterenko, T. V., Shikhov, V. N., Forti, Giorgio, Furia, Alberto, Finazzi, Giovanni, Barbagallo, Romina Paola, Agalarov, R., Gasanov, R., Iskenderova, S., Nobuhiro, G. O., Osamu, Miyashita, Ramrakhiani, M., Soni, R. K., Yoshida, Masasuke, Akutsu, Hideo, Yagi, Hiromasa, Tozawa, Kacko, Sekino, Nobuaki, Iwabuchi, Tomoyuki, Kaulen, A. D., Avetisyan, A. V., Feniouk, B. A., Skulachev, V. P., Breyton, Cécile, Kühlbrandt, Werner, Gräslund, Astrid, Assarsson, Maria, Libisch, B., Horváth, G., Gombos, Z., Budagovskaya, N. V., Kudryasheva, N., Fukunishi, Arima, Harada, Erisa, Fukuoka, Yuki, Ohmura, Tomoaki, Kawai, Gota, Watanabe, Kimitsuna, Žekš, Boštjan, Božič, Bojan, Derganc, Jure, Svetina, Saša, Hoh, J. F. Y., Li, Z. B., Rossmanith, G. H., Frederix, P. L. T. M., de Beer, E. L., Treijtel, B. W., Blangè, T., Galtet, F., Hénon, S., Isabey, D., Planus, E., Laurent, V., Rath, L. S., Raval, M. K., Dash, P. K., Ramakrishnan, C., Balaram, R., Basak, Kanika, Balaban, Alexandra T., Nandy, Ashesh, Grunwald, Gregory D., Vracko, Marjan, Randic, Milan, Basak, Subhash C., Amic, Dragan, Beslo, Drago, Trinajstic, Nenad, Nikolic, Sonja, Walahaw, J., Lensink, Marc F. J., Reddy, Boojala V. B., Shindylov, Ilya N., Bourne, Philip E., Grigera, J. R., de Xammar Oro, J., Donnamaria, M. C., Neagu, Monica, Neagu, Adrian, Janežič, Dušanka, Praprotnik, Matej, Nilsson, Lennart, Mark, Pekka, Fata, La L., Dardenne, Laurent E., Werneck, Araken S., Neto, Marçal de O., Kannan, N., Vishveshwara, S., Veluraja, K., Opitz, David, Balasubramanian, Krishnan, Gute, Brian D., Mills, Denise, Lungeanu, Diana, Mihalas, G. I., Macovievici, G., Gruia, Raluca, Dalcin, B., Cortez-Maghelly, C., Passos, E. P., Ljubisavljevic, M., Blesic, S., Milosevic, S., Stratimirovic, D. J., Bachhawat, Nandita, Mande, Shekhar C., Nandy, A., Nishigaki, Koichi, Saito, Ayumu, Naimuddin, Mohammed, Takaesu, Hirotomo, Ono, Mitsuo, Hirokawa, Takatsugu, Eissa, A. M., Ahmed, Abdalla S., El Gohary, M. I., Nakashima, Hiroshi, Raghava, G. P. S., Kurgalvuk, N., Goryn, O., Gerstman, Bernard S., Kratasyuk, V. A., Esimbekova, E. N., Gritsenko, E. V., Remmel, N. N., Maznyak, O. M., German, A., Tikhonov, A., Tchitchkan, D., Koulchitsky, S., Pashkevich, S., Pletnev, S., Kulchitsky, V., Pesotskaya, Y., Shapiro, Erik M., Borthakur, Arijitt, Dimitrov, Ivan, Leigh, John S., Rizi, Rahim, Reddy, Ravinder, Charagundla, Sridhar, Duvvuri, Umamaheswar, Degaonkar, M., Khubchandani, M., Kumar, Mahesh, Jagannathan, N R., Raghunathan, P., Jayasundar, Rama, Coshic, O., Rath, O. K., Julka, P. K., Iliescu, Karina Roxana, Sajin, Maria, Petcu, Ileana, Moisoi, Nicolcta, Kuzmenko, A. I., Donchenko, G. V., Nikolenko, I. A., Morozova, R. P., Rahman, M. K., Ahmed, M. M., Watanabe, Takehiro, Uretzky, G., Ammar, R., Sharony, R., Rubin, Y., Gilboa, H., Mallick, H. N., Kumar, Mohan V., Begum, Gulnaz M., Degaonkar, Mahaveer N., Govindasamy, S., Kumosani, T. A., Lupusoru, C., Titescu, G., Haulica, I., Stefanescu, I., Iliescu, R., Nastasa, V., Bild, W., Khetawat, Gopal, Nealen, M., Faraday, N., Bray, P. F., Noga, S., Lycholat, E. A., Ananieva, T. V., Kosevich, M V., Stepanyan, S. G., Antonyuk, S. V., Khachatryan, A., Kumar, A., Arakelian, H., Khachatryan, R., Agadjanyan, S., Ayrapetyan, S., Mkheyan, V., Rajan, S. S., Kabaleeswaran, V., Gopalakrishnan, Geetha, Govindachari, T. R., Ramrakhiani, Meera, Cullen, David C., Lowe, Phillip, Badley, Andrew, Hermel, H., Möhwald, H., Schmahl, W., Singh, Anil K., Das, Joydip, Majumdar, Nirmalya, Dér, András, Oroszi, László, Kelemen, Loránd, Ormos, Pál, Hámori, András, Ramsden, Jeremy J., Mitra, Chanchal K., Savitri, D., Yanagida, Toshio, Esaki, Seiji, Sowa, Yosiyuki, Nishida, Tomoyuki, Kimura, Yuji, Radu, M., Laukhina, E. E., Kasumova, L. A., Koltover, V. K., Bubnov, V. P., Estrin, Ya. I., Dotta, Rajiv, Zahradník, Ivan, Marko, Milan, Novák, Pavel, Miyata, Hidetake, Hirata, Hiroaki, Sengupta, P., Maiti, S., Balaji, J., Banerjee, S., Barker, A. L., Winlove, C. P., OʼHare, D., Macpherson, J. V., Gonsalves, M., Unwin, P. R., Phillip, R., Kumar, Ravindra G., Murata, K., Nagayaka, K., Danev, R., Sugitani, S., Gősch, Michael, Thyberg, P., Földes-Papp, Z., Björk, G., Blom, H., Holm, J., Heino, T., Inagaki, Fuyuhiko, Yokochi, Masashi, Kusunoki, Masami, Matthews, E. K., Pines, J., Chukova, Yu. P., Koltover, Vitaly K., Kang, B. P. S., Bansal, Geetanjali, Bansal, M. P., Singh, U., Singh, Uma, Nakata, Kotoko, Nakano, Tastuya, Kaminuma, Tsuguchika, Kirn, Bonn, Potocnik, Neja, Stare, Vito, Shukla, Latal, Sastry, M. D., Natarajan, V., Devasagayam, T. P. A., Kesavan, P. C., Sayfutdinov, R., Degermendzhy, A. G., Adamovich, V. V., Rogozin, Yu. D., Khetrapal, C. L., Gowda, G. A. Nagana, Ghimire, Kedar Nath, Masaru, Ishida, Fujita, H., Ishiwata, S., Suzuki, M., Kawahara, S., Kirino, Y., Kishimoto, Y., Mori, H., Mishina, M., Ohshima, H., Dukhin, A. S., Goetz, P. J., Shilov, V. N., and Mishra, R. K.

Published
1999
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25. Tetrapeptide KEDW Interacts with DNA and Regulates Gene Expression.

Author

Khavinson, V. Kh., Tendler, S. M., Kasyanenko, N. A., Tarnovskaya, S. I., Linkova, N. S., Ashapkin, V. V., Yakutseni, P. P., and Vanyushin, B. F.

Subjects
PEPTIDES, DIABETES, PROTEIN synthesis
Abstract

Peptide KEDW (Lys-Glu-Asp-Trp-NH2) is known to reduce the blood glucose level in rats with streptozotocin- and alloxan-induced diabetes mellitus. Here, we examine the influence of KEDW peptide on cell differentiation and DNA structure. KEDW peptide increased the expression of PDX1, NGN3, PAX6, FOXA2, NKX2-2, NKX6.1, and PAX4 genes but decreased MNX1 and HOXA3 gene expression when added to pancreatic cell culture. Moreover, KEDW peptide caused an increase in expression of PDX1, NGN3, PAX6, FOXA2, NKX2-2, NKX6.1, and PAX4 proteins without affecting synthesis of MNX1 and HOXA3 when added to pancreatic cell culture. Results obtained through physical methods (UV-visible absorption, circular dichroism) and molecular modelling methods suggest that the peptide binds to DNA along the major groove. Experimental and theoretical data provided a 3D model of the stable DNA-peptide complex. We propose that regulation of differentiation factor expression in pancreatic (endocrine) cells by KEDW peptide occurs through specific binding of the peptide to regulatory elements of corresponding genes. [ABSTRACT FROM AUTHOR]

Published
2015
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26. Conformational and phase transitions in DNA-photosensitive surfactant solutions: Experiment and modeling.

Author

Kasyanenko, N., Lysyakova, L., Ramazanov, R., Nesterenko, A., Yaroshevich, I., Titov, E., Alexeev, G., Lezov, A., and Unksov, I.

Abstract

ABSTRACT DNA binding to trans- and cis-isomers of azobenzene containing cationic surfactant in 5 m M NaCl solution was investigated by the methods of dynamic light scattering (DLS), low-gradient viscometry (LGV), atomic force microscopy (AFM), circular dichroism (CD), gel electrophoresis (GE), flow birefringence (FB), UV-Vis spectrophotometry. Light-responsive conformational transitions of DNA in complex with photosensitive surfactant, changes in DNA optical anisotropy and persistent length, phase transition of DNA into nanoparticles induced by high surfactant concentration, as well as transformation of surfactant conformation under its binding to macromolecule were studied. Computer simulations of micelles formation for cis- and trans-isomers of azobenzene containing surfactant, as well as DNA-surfactant interaction, were carried out. Phase diagram for DNA-surfactant solutions was designed. The possibility to reverse the DNA packaging induced by surfactant binding with the dilution and light irradiation was shown. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 109-122, 2015. [ABSTRACT FROM AUTHOR]

Published
2015
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30. Contributory presentations/posters

Author

Manoj, N., Srinivas, V., Surolia, A., Vijayan, M., Suguna, K., Ravishankar, R., Suguna, K., Surolia, A., Vijayan, M., Schwarzenbacher, R., Zeth, K., Diederichs, Kostner, G., Gries, A., Laggner, P., Prassl, R., Madhusudan, Akamine, Pearl, Xuong, Nguyen-huu, Taylor, Susan, Sagar, M., Ravishankar, R., Saikrishnan, K., Roy, S., Purnapatre, K., Handa, P., Varshney, U., Vijayan, M., Biswal, B., Sukumar, N., Vijayan, M., Rao, J., Johnson, A., Pattabhi, Vasantha, Krishna, S., Sastri, Mira, Savithri, H., Murthy, M., Pillai, Bindu, Kannan, Hosur, M., Kumar, Mukesh, Patwardhan, Swati, Kannan, K., Hosur, M., Padmanabhaa, B., Sasaki-Sugio, S., Nukaga, M., Matsuzaki, T., Karthikevan, S., Sharma, S., Sharma, A., Paramasivam, M., Kumar, P., Khan, J., Yadav, S., Srinivasan, A., Singh, T., Gourinath, S., Alam, Neelima, Srintvasan, A., Singh, T., Chandra, Vikas, Kaur, Punit, Betzel, Ch., Singh, T., Ghosh, S., Bera, A., Bhattacharya, S., Chakraborty, S., Pal, A., Mukhopadhyay, B., Dey, I., Haldar, U., Baneriee, Asok, Sevcik, Jozef, Solovicova, Adriana, Sekar, K., Sundaralingam, M., Betzel, Ch., Genov, N., Singh, T., Liang, Dong-cai, Jiang, Tao, Zhang, Ji-ping, Chang, Wen-rui, Jahnke, Wolfgang, Blommers, Marcel, Panchal, S., Hosur, R., Pillay, Bindu, Hosur, M., Mathur, Puniti, Srivatsun, S., Joshi, Ratan, Jaganathan, N., Chauhan, V., Atreya, H., Sahu, S., Chary, K., Govil, Girjesh, Adjadj, Elisabeth, Quinjou, Éric, Izadi-Pruneyre, Nadia, Blouquit, Yves, Mispelter, Joël, Heyd, Bernadette, Lerat, Guilhem, Milnard, Philippe, Desmadreil, Michel, Lin, Y., Rao, B., Raghunathan, Vidva, Chau, Mei, Rao, B., Pesais, Prashant, Srivastava, Sudha, Coutinho, Evans, Saran, Anil, Sapico, Leizl, Gesme, Jayson, Lijima, Herbert, Paxton, Raymond, Srikrishnan, Thamarapu, Grace, C., Nagenagowda, G., Lynn, A., Cowsik, Sudha, Sahu, Sarata, Chauhan, S., Bhattacharya, A., Chary, K., Govil, G., Kumar, Anil, Pellecchia, Maurizio, Zuiderweg, Erik, Kawano, Keiichi, Aizawa, Tomoyasu, Fujitani, Naoki, Hayakawa, Yoichi, Ohnishi, Atsushi, Ohkubo, Tadayasu, Kumaki, Yasuhiro, Hikichi, Kunio, Nitta, Katsutoshi, Rani Parvathy, V., Chary, K., Kini, R., Govil, G., Koshiba, Takumi, Kobashigawa, Yoshihiro, Yao, Min, Demura, Makoto, Nakagawa, Astushi, Tanaka, Isao, Kuwajima, Kunihiro, Nitta, Katsutoshi, Linge, Jens, Donoghue, Seán, Nilges, Michael, Chakshusmathi, G., Ratnaparkhi, Girish, Madhu, P., Varadarajan, R., Tetreau, C., Tourbez, M., Lavalette, D., Manno, M., Biagio, P., Martorana, V., Emanuele, A., Vaiana, S., Bulone, D., Palma-Vittorelli, M., Palma, M., Trivedi, V., Cheng, S., Chien, W., Yang, S., Francis, S., Chang, D., Batra, Renn, Geeves, Michael, Manstein, Dietmar, Trvlska, Joanna, Grochowski, Pawel, Geller, Maciej, Ginalski, K., Grochowski, P., Lesyng, B., Lavalette, P., Tetreau, C., Tourbez, M., Blouquit, Y., Roccatano, D., Amadei, A., Nola, A., Berendsen, H., Ho, Bosco, Curmi, P., Berry, H., Lairez, D., Pauthe, E., Pelta, J., Kothekar, V., Sahi, Shakti, Srinivasan, M., Singh, Anil, Madhusudnan, Kartha, Nandel, Fateh, Kaur, Harpreet, Nandel, Fateh, Singh, Balwinder, Jain, D., Feenstra, K., Berendsen, Herman, Tama, F., Sanejouand, Y., Go, N., Sharma, Deepak, Sharma, Sunita, Pasha, Santosh, Brahmachari, Samir, Viiavaraghavan, R., Makker, Jyoti, Dey, Sharmisllia, Kumar, S., Singh, T., Lakshmikanth, G., Krishnamoorthy, G., Mazhul, V., Zaitseva, E., Kierdaszuk, Borys, Widengren, J., Terry, B., Mets, Ü., Rigler, R., Swaminathan, R., Thamotharan, S., Yathindra, N., Shibata, Y., Chosrowjan, H., Mataga, N., Morisima, I., Chakraharty, Tania, Xiao, Ming, Cooke, Roger, Selvin, Paul, Branca, C., Faraone, A., Magazù, S., Maisano, G., Migliardo, P., Villari, V., Behere, Digambar, Deva, M., Brunori, M., Cutruzzolà, F., Gibson, Q., Savino, C., Travaglini-Allocatelli, C., Vallone, B., Prasad, Swati, Mazumdar, Shyamalava, Mitra, Samaresh, Soto, P., Fayad, R., Sukovataya, I., Tyulkova, N., Mamedov, Sh., Aktas, B., Canturk, M., Aksakal, B., Yilgin, R., Bogutska, K., Miroshnichenko, N., Chacko, S., DiSanto, M., Hypolite, J., Zheng, Y-M., Wein, A., Wojciechowski, M., Grycuk, T., Antosiewicz, J., Lesyng, B., Ceruso, Marc, Nola, Alfredo, Bandvopadhvay, Subhasis, Chatterjee, Bishnu, Choudhury, Devapriva, Thompson, Andrew, Stojanoff, Vivian, Pinkner, Jerome, Hultgren, Scott, Khight, Stefan, Flatters, Delphine, Goodfellow, Julia, Takazawatt, Fumi, Kanehisa, Minoru, Sasai, Masaki, Nakamura, Hironori, Sasai, Masaki, Han, Wang, Zheng, Yuan, Xin, Wang, Min, Pan, Bhakuni, Vlnod, Kulkarni, Sangeeta, Ahmad, Atta, Prakash, Koodathingal, Prajapati, Shashi, Surin, Alexey, Matsumoto, Tomoharu, Yang, Li, Nakagawa, Yuki, Kimura, Kazumoto, Amemiya, Yoshiyuki, Semisotnov, Gennady, Kihara, Hiroshi, Tayyab, Saad, Muzammil, Salman, Kumar, Yogesh, Kulkarni, Sangeeta, Prajapati, Shashi, Prakash, Koodathingal, Ahmad, Atta, Bhakuni, Vinod, Sundd, Monica, Kundu, Suman, Jagannadham, M., Kundu, Suman, Sundd, Monica, Jagannadham, Medicherla, Chandani, Bina, Dhar, Ruby, Sinha, Lalankumar, Warrier, Deepti, Mehrotra, Sonam, Khandelwal, Purnima, Seth, Subhendu, Hosur, R., Sasidhar, Y., Prabha, C., Gidwani, Arun, Ahmad, Atta, Kulkarni, Sangeeta, Madhusudan, K., Bhakuni, Vinod, Kinjo, Akira, Nishikawa, Ken, Chakravarty, Suvobrata, Varadarajan, Raghavan, Noyelle, K., Haezebrouck, P., Joniau, M., Dael, H., Dash, Sheffali, Jha, Indra, Bhat, Rajiv, Mohanty, Prasanna, Bandyopadhyay, A., Sonawat, H., Rao, Ch., Datta, Siddhartha, Rajaraman, K., Raman, B., Ramakrishna, T., Rao, Ch., Pande, A., Pande, J., Betts, S., Asherie, N., Ogun, O., King, J., Benedek, G., Sokolova, I., Tyulkova, N., Kalacheva, G., Sonoyama, Masashi, Yokoyama, Yasunori, Taira, Kunihiro, Mitaku, Shigeki, Nakazawal, Chicko, Sasakil, Takanori, Mukai, Yuri, Kamo, Naoki, Sonoyama, Masashi, Mitaku, Shigeki, Dalal, Seema, Regan, Lynne, Mukai, Yuri, Kamo, Naoki, Mituku, Shigeki, Roychoudhury, Mihir, Kumar, Devesh, Lőrinczv, Dénes, Könczöl, Franciska, Farkas, László, Belagyi, Joseph, Schick, Christoph, Thomson, Christy, 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Published
1999
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32. pH-dependent binding of ATP aptamer to the target and competition strands: Fluorescent melting curve fitting study.

Author

Gabrusenok PV, Ramazanov RR, Kasyanenko NA, Lantushenko AO, and Sokolov PA

Subjects
Hydrogen-Ion Concentration, Binding, Competitive, Nucleic Acid Denaturation, Aptamers, Nucleotide chemistry, Aptamers, Nucleotide metabolism, Adenosine Triphosphate metabolism, Adenosine Triphosphate chemistry, Thermodynamics
Abstract

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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Published
2024
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33. Sup35NMp morphology evaluation on Au, Si, formvar and mica surfaces using AFM, SEM and TEM.

Author

Sokolov PA, Bondarev SA, Belousov MV, Zhouravleva GA, and Kasyanenko NA

Subjects
Adsorption, Aluminum Silicates chemistry, Amyloid ultrastructure, Gold chemistry, Microscopy, Atomic Force methods, Microscopy, Electron, Scanning methods, Microscopy, Electron, Transmission methods, Peptide Termination Factors ultrastructure, Prions ultrastructure, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae ultrastructure, Saccharomyces cerevisiae Proteins ultrastructure, Silicon Dioxide chemistry, Surface Properties, Amyloid chemistry, Peptide Termination Factors chemistry, Prions chemistry, Saccharomyces cerevisiae chemistry, Saccharomyces cerevisiae Proteins chemistry
Abstract

Prion and some other incurable human neurodegenerative diseases are associated with misfolding of specific proteins, followed by the formation of amyloids. Despite the widespread usage of the transmission electron and of the atomic force microscopy for studing such amyloids, many related methodological issues still have not been studied until now. Here, we consider one of the first amyloids found in Saccharomyces cerevisiae yeast, i.e. Sup35NMp, to study the adsorption of monomeric protein and its fibrils on the surface of mica, silica, gold and on formvar film. Comparison of linear characteristics of these units calculated by processing of images obtained by the atomic force, transmission and scanning electron microscopy was carried out. The minimal number of measurements of fibril diameters to obtain the values in a given confidence interval were determined. We investigated the film formed by monomeric protein on mica surface, which veiled some morphology features of fibrils. Besides, we revealed that parts of the Sup35NMp excluded from the fibril core can form a wide "coat". The length of the protein forming the core of the fibrils was estimated., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Published
2018
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34. DNA-polycation complexes: effect of polycation structure on physico-chemical and biological properties.

Author

Slita AV, Kasyanenko NA, Nazarova OV, Gavrilova II, Eropkina EM, Sirotkin AK, Smirnova TD, Kiselev OI, and Panarin EF

Subjects
Animals, Cell Line, Cell Line, Tumor, Cell Survival drug effects, Cells drug effects, Chemical Phenomena, Chemistry, Physical, Genes, Reporter, Humans, Macromolecular Substances chemistry, Molecular Structure, Polyamines pharmacology, Polyamines toxicity, Polyelectrolytes, Structure-Activity Relationship, Transfection, DNA chemistry, DNA metabolism, Polyamines chemistry
Abstract

The purpose of the study was to investigate the influence of cationic polymer structure on the formation of DNA-polycation complexes and their transfection activity. Primary, tertiary, and quaternary polyamines with molecular masses ranging from 8000 to 200,000 were investigated. DNA-cationic polymer interaction was characterized by low gradient viscometry, dynamic light scattering, circular dichroism, UV spectrometry, flow birefringence, DNA electrophoresis, and electron microscopy. Transfection activity of the complexes was evaluated by the expression of reporter gene (beta-galactosidase) and using synthetic FITC-labelled oligonucleotides. Complex formation was found to be dependent on the structure and molecular weight of the polymer and the ionic strength of the solution. Secondary DNA structure in complexes was not disrupted, and DNA was protected from protonation. Cell lines of different origin were used for testing of transfection activity of the complexes. The sensitivity of the cells to transfection was established to be highly dependent on the cell line. DNA-polycation complexes are non-toxic according to MTT. Polyallylamine, and polydimethylaminoethylmethacrylate were found to be the most promising polycations for gene delivery. Transfection efficacy of their complexes with DNA to T-98G cells reaches up to 90-100%. It was found that optimal molecular mass of polydimethylaminoethylmethacrylate is in the range of 8000-50,000 Da.

Published
2007
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