Skip to main content
SpringerLink
Log in

Complexes and Supramolecular Associates of Dodecyl-Containing Oligonucleotides with Serum Albumin

  • Published:
Biochemistry (Moscow) Aims and scope Submit manuscript

Abstract

Serum albumin is currently in the focus of biomedical research as a promising platform for the creation of multicomponent self-assembling systems due to the presence of several sites with high binding affinity of various compounds in its molecule, including lipophilic oligonucleotide conjugates. In this work, we investigated the stoichiometry of the dodecyl-containing oligonucleotides binding to bovine and human serum albumins using an electrophoretic mobility shift assay. The results indicate the formation of the albumin-oligonucleotide complexes with a stoichiometry of about 1 : (1.25 ± 0.25) under physiological-like conditions. Using atomic force microscopy, it was found that the interaction of human serum albumin with the duplex of complementary dodecyl-containing oligonucleotides resulted in the formation of circular associates with a diameter of 165.5 ± 94.3 nm and 28.9 ± 16.9 nm in height, and interaction with polydeoxyadenylic acid and dodecyl-containing oligothymidylate resulted in formation of supramolecular associates with the size of about 315.4 ± 70.9 and 188.3 ± 43.7 nm, respectively. The obtained data allow considering the dodecyl-containing oligonucleotides and albumin as potential components of the designed self-assembling systems for solving problems of molecular biology, biomedicine, and development of unique theranostics with targeted action.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.
Fig. 6.

Similar content being viewed by others

Abbreviations

AFM:

atomic force microscopy

BSA:

bovine serum albumin

DCO:

dodecyl-containing oligonucleotide

eqv.:

equivalent

FA:

fatty acids

FAM:

6-carboxyfluorescein residue

HSA:

human serum albumin

HSAM :

the purified monomeric fraction of HSA

NA:

nucleic acids

poly(dA):

polydeoxyadenylic acid

SA:

serum albumin

tNA:

therapeutic nucleic acids

References

  1. Smith, C. I. E., and Zain, R. (2019) Therapeutic oligonucleotides: state of the art, Annu. Rev. Pharmacol. Toxicol., 59, 605-630, https://doi.org/10.1146/annurev-pharmtox-010818-021050.

    Article  CAS  PubMed  Google Scholar 

  2. Roberts, T. C., Langer, R., and Wood, M. J. A. (2020) Advances in oligonucleotide drug delivery, Nat. Rev Drug. Discov., 19, 673-694, https://doi.org/10.1038/s41573-020-0075-7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Gökirmak, T., Nikan, M., Wiechman, S., Prakash, T. P., Tanowitz, M., and Seth, P. P. (2021) Overcoming the challenges of tissue delivery for oligonucleotide therapeutics, Trends Pharmacol. Sci., 42, 588-604, https://doi.org/10.1016/j.tips.2021.04.010.

    Article  CAS  PubMed  Google Scholar 

  4. Bakowski, K., and Vogel, S. (2022) Evolution of complexity in non-viral oligonucleotide delivery systems: from gymnotic delivery through bioconjugates to biomimetic nanoparticles, RNA Biol., 19, 1256-1275, https://doi.org/10.1080/15476286.2022.2147278.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Crooke, S. T., Baker, B. F., Crooke, R. M., and Liang, X.-H. (2021) Antisense technology: an overview and prospectus, Nat. Rev Drug. Discov., 20, 427-453, https://doi.org/10.1038/s41573-021-00162-z.

    Article  CAS  PubMed  Google Scholar 

  6. Mullard, A. (2023) 2022 FDA approvals, Nat. Rev Drug. Discov., 22, 83-88, https://doi.org/10.1038/d41573-023-00001-3.

    Article  CAS  PubMed  Google Scholar 

  7. Egli, M., and Manoharan, M. (2023) Chemistry, structure and function of approved oligonucleotide therapeutics, Nucleic Acids Res., 51, 2529-2573, https://doi.org/10.1093/nar/gkad067.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Juliano, R. L. (2016) The delivery of therapeutic oligonucleotides, Nucleic Acids Res., 44, 6518-6548, https://doi.org/10.1093/nar/gkw236.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Juliano, R. L. (2021) Manipulation of the endosome trafficking machinery: implications for oligonucleotide delivery, Biomedicines, 9, 512, https://doi.org/10.3390/biomedicines9050512.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Tran, P., Weldemichael, T., Liu, Z., and Li, H.-Yu (2022) Delivery of oligonucleotides: efficiency with lipid conjugation and clinical outcome, Pharmaceutics, 14, 342, https://doi.org/10.3390/pharmaceutics14020342.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Kupryushkin, M. S., Pyshnyi, D. V., and Stetsenko, D. A. (2014) Phosphoryl guanidines: A new type of nucleic acid analogues, Acta Naturae, 6, 116-118, https://doi.org/10.32607/20758251-2014-6-4-116-118.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Lomzov, A. A., Kupryushkin, M. S., Shernyukov, A. V., Nekrasov, M. D., Dovydenko, I. S., Stetsenko, D. A., and Pyshnyi, D. V. (2019) Diastereomers of a mono-substituted phosphoryl guanidine trideoxyribonucleotide: isolation and properties, Biochem. Biophys. Res. Commun., 513, 807-811, https://doi.org/10.1016/j.bbrc.2019.04.024.

    Article  CAS  PubMed  Google Scholar 

  13. Miroshnichenko, S. K., Patutina, O. A., Burakova, E. A., Chelobanov, B. P., Fokina, A. A., Vlassov, V. V., Altman, S., Zenkova, M. A., and Stetsenko, D. A. (2019) Mesyl phosphoramidate antisense oligonucleotides as an alternative to phosphorothioates with improved biochemical and biological properties, Proc. Natl. Acad. Sci. USA, 116, 1229-1234, https://doi.org/10.1073/pnas.1813376116.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Pavlova, A. S., Yakovleva, K. I., Epanchitseva, A. V., Kupryushkin, M. S., Pyshnaya, I. A., Pyshnyi, D. V., Ryabchikova, E. I., and Dovydenko, I. S. (2021) An influence of modification with phosphoryl guanidine combined with a 2′-O-methyl or 2′-fluoro group on the small-interfering-RNA effect, Int. J. Mol. Sci., 22, 9784, https://doi.org/10.3390/ijms22189784.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Anderson, B. A., Freestone, G. C., Low, O., De-Hoyos, C. L., Drury, III, W. J., Østergaard, M. E., Migawa, M. T., Fazio, M., Wan, W. B., Berdeja, A., Scandalis, E., Burel, S. A., Vickers, T. A., Crooke, S. T., Swayze, E. E., Liang, X., and Seth, P. P. (2021) Towards next generation antisense oligonucleotides: mesylphosphoramidate modification improves therapeutic index and duration of effect of gapmer antisense oligonucleotides, Nucleic Acids Res., 49, 9026-9041, https://doi.org/10.1093/nar/gkab718.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Kandasamy, P., Liu, Y., Aduda, V., Akare, S., Alam, R., Andreucci, A., Boulay, D., Bowman, K., Byrne, M., Cannon, M., Chivatakarn, O., Shelke, J. D., Iwamoto, N., Kawamoto, T., Kumarasamy, J., Lamore, S., Lemaitre, M., Lin, X., Longo, K., Looby, R., Marappan, S., Metterville, J., Mohapatra, S., Newman, B., Paik, I.-H., Patil, S., Purcell-Estabrook, E., Shimizu, M., Shum, P., Standley, S., Taborn, K., Tripathi, S., Yang, H., Yin, Y., Zhao, X., Dale, E., and Vargeese, S. (2022) Impact of guanidine-containing backbone linkages on stereopure antisense oligonucleotides in the CNS, Nucleic Acids Res., 50, 5401-5423, https://doi.org/10.1093/nar/gkac037.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Hall, J. (2023) Future directions for medicinal chemistry in the field of oligonucleotide therapeutics, RNA, 29, 423-433, https://doi.org/10.1261/rna.079511.122.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Godfrey, C., Desviat, L. R., Smedsrød, B., Piétri-Rouxel, F., Denti, M. A., Disterer, P., Lorain, S., Nogales-Gadea, G., Sardone, V., Anwar, R., Andaloussi, S. E., Lehto, T., Khoo, B., Brolin, C., van Roon-Mom, W. M. C., Goyenvalle, A., Aartsma-Rus, A., and Arechavala-Gomeza, V. (2017) Delivery is key: lessons learnt from developing splice-switching antisense therapies, EMBO Mol. Med., 9, 545-557, https://doi.org/10.15252/emmm.201607199.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Gaus, H. J., Gupta, R., Chappell, A. E., Østergaard, M. E., Swayze, E. E., and Seth, P. P. (2019) Characterization of the interactions of chemically-modified therapeutic nucleic acids with plasma proteins using a fluorescence polarization assay, Nucleic Acids Res., 47, 1110-1122, https://doi.org/10.1093/nar/gky1260.

    Article  CAS  PubMed  Google Scholar 

  20. Lacroix, A., Fakih, H. H., and Sleiman, H. F. (2020) Detailed cellular assessment of albumin-bound oligonucleotides: Increased stability and lower non-specific cell uptake, J. Control. Release, 324, 34-46, https://doi.org/10.1016/j.jconrel.2020.04.020.

    Article  CAS  PubMed  Google Scholar 

  21. Crooke, S. T., Seth, P. P., Vickers, T. A., and Liang, X.-H. (2020) The interaction of phosphorothioate-containing RNA targeted drugs with proteins is a critical determinant of the therapeutic effects of these agents, J. Am. Chem. Soc., 142, 14754-14771, https://doi.org/10.1021/jacs.0c04928.

    Article  CAS  PubMed  Google Scholar 

  22. Kim, W., Ly, N. K., He, Y., Li, Y., Yuan, Zh., and Yeo, Y. (2023) Protein corona: friend or foe? Co-opting serum proteins for nanoparticle delivery, Adv. Drug Deliv. Rev., 192, 114635, https://doi.org/10.1016/j.addr.2022.114635.

    Article  CAS  PubMed  Google Scholar 

  23. Chen, Z., Chen, X., Huang, J., Wang, J., and Wang, Z. (2022) Harnessing protein corona for biomimetic nanomedicine design, Biomimetics, 7, 126, https://doi.org/10.3390/biomimetics7030126.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Chernikov, I. V., Gladkikh, D. V., Meschaninova, M. I., Ven’yaminova, A. G., Zenkova, M. A., et al. (2017) Cholesterol-containing nuclease-resistant siRNA accumulates in tumors in a carrier-free mode and silences MDR1 gene, Mol. Ther., 6, 209-220, https://doi.org/10.1016/j.omtn.2016.12.011.

    Article  CAS  Google Scholar 

  25. Prakash, T. P., Mullick, A. E., Lee, R. G., Yu, J., Yeh, S. T., Low, A., Chappell, A. E., Østergaard, M. E., Murray, S., Gaus, H. J., Swayze, E. E., and Seth, P. P. (2019) Fatty acid conjugation enhances potency of antisense oligonucleotides in muscle, Nucleic Acids Res., 47, 6029-6044, https://doi.org/10.1093/nar/gkz354.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Benizri, S., Gissot, A., Martin, A., Vialet, B., Barthelemy, P., and Grinstaff, M. W. (2019) Bioconjugated oligonucleotides: recent developments and therapeutic applications, Bioconjugate Chem., 30, 366-383, https://doi.org/10.1021/acs.bioconjchem.8b00761.

    Article  CAS  Google Scholar 

  27. Kupryushkin, M. S., Zharkov, T. D., Ilina, E. S., Markov, O. V., Kochetkova, A. S., Akhmetova, M. M., Lomzov, A. A., Pyshnyi, D. V., Lavrik, O. A., and Khodyreva, S. N. (2021) Triazinylamidophosphate oligonucleotides: synthesis and study of their interaction with cells and DNA-binding proteins, Russ. J. Bioorganic Chem., 47, 719-733, https://doi.org/10.1134/S1068162021030110.

    Article  CAS  Google Scholar 

  28. Brown, K. M., Nair, J. K., Janas, M. M., Anglero-Rodriguez, Y. I., Dang, L. T. H., Peng, H., Theile, C. S., Castellanos-Rizaldos, E., Brown, C., Foster, D., Kurz, J., Allen, J., Maganti, R., Li, J., Matsuda, S., Stricos, M., Chickering, T., Jung, M., Wassarman, K., Rollins, J., Woods, L., Kelin, A., Guenther, D. C., Mobley, M. W., Petrulis, J., McDougall, R., Racie, T., Bombardie, J., Cha, D., Agarwal, S., Johnson, L., Jiang, Y., Lentini, S., Gilbert, J., Nguyen, T., Chigas, S., LeBlanc, S., Poreci, U., Kasper, A., Rogers, A. B., Chong, S., Davis, W., Sutherland, J. E., Castonero, A., Milstein, S., Schlegel, M. K., Zlatev, I., Charisse, K., Keating, M., Manoharan, M., Fitzgerald, K., Wu, J.-T., Maier, M. A., and Jadhav, V. (2022) Expanding RNAi therapeutics to extrahepatic tissues with lipophilic conjugates, Nat. Biotechnol., 40, 1500-1508, https://doi.org/10.1038/s41587-022-01334-x.

    Article  CAS  PubMed  Google Scholar 

  29. Biscans, A., Caiazzi, J., McHugh, N., Hariharan, V., Muhuri, M., and Khvorova, A. (2021) Docosanoic acid conjugation to siRNA enables functional and safe delivery to skeletal and cardiac muscles, Mol. Ther., 29, 1382-1394, https://doi.org/10.1016/j.ymthe.2020.12.023.

    Article  CAS  PubMed  Google Scholar 

  30. Sarrett, S. M., Werfel, T. A., Lee, L., Jackson, M. A., Kilchrist, K. V., Brantley-Sieders, D., and Duvall, C. L. (2017) Lipophilic siRNA targets albumin in situ and promotes bioavailability, tumor penetration, and carrier-free gene silencing, Proc. Natl. Acad. Sci. USA, 114, E6490-E6497, https://doi.org/10.1073/pnas.1621240114.

    Article  CAS  Google Scholar 

  31. Jin, C., Zhang, H., Zou, J., Liu, Y., Zhang, L., Li, F., Wang, R., Xuan, W., Ye, M., and Tan, W. (2018) Floxuridine homomeric oligonucleotides “Hitchhike” with albumin in situ for cancer chemotherapy, Angew. Chem. Int. Ed., 57, 8994-8997, https://doi.org/10.1002/anie.201804156.

    Article  CAS  Google Scholar 

  32. Chappell, A. E., Gaus, H. J., Berdeja, A., Gupta, R., Jo, M., Prakash, T. P., Oestergaard, E. E., Swayze, E. E., and Seth, P. P. (2020) Mechanisms of palmitic acid-conjugated antisense oligonucleotide distribution in mice, Nucleic Acids Res., 48, 4382-4395, https://doi.org/10.1093/nar/gkaa164.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Sleep, D. (2015) Albumin and its application in drug delivery, Expert Opin. Drug Deliv., 12, 793-812, https://doi.org/10.1517/17425247.2015.993313.

    Article  CAS  PubMed  Google Scholar 

  34. Hoogenboezem, E. N., and Duvall, C. L. (2018) Harnessing albumin as a carrier for cancer therapies, Adv. Drug Deliv. Rev., 130, 73-89, https://doi.org/10.1016/j.addr.2018.07.011.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Varanko, A., Saha, S., and Chilkoti, A. (2020) Recent trends in protein and peptide-based biomaterials for advanced drug delivery, Adv. Drug Deliv. Rev., 156, 133-187, https://doi.org/10.1016/j.addr.2020.08.008.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Prajapati, R., and Somoza, Á. (2021) Albumin nanostructures for nucleic acid delivery in cancer: current trend, emerging issues, and possible solutions, Cancers, 13, 3454, https://doi.org/10.3390/cancers13143454.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Chubarov, A. S. (2022) Serum albumin for magnetic nanoparticles coating, Magnetochemistry, 8, 13, https://doi.org/10.3390/magnetochemistry8020013.

    Article  CAS  Google Scholar 

  38. Hu, H., Quintana, J., Weissleder, R., Parangi, S., and Miller, M. (2022) Deciphering albumin-directed drug delivery by imaging, Adv. Drug Deliv. Rev., 185, 114237, https://doi.org/10.1016/j.addr.2022.114237.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Merlot, A. M., Kalinowski, D. S., and Richardson, D. R. (2014) Unraveling the mysteries of serum albumin – more than just a serum protein, Front. Physiol., 5, 299, https://doi.org/10.3389/fphys.2014.00299.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Zhao, P., Wang, Y., Wu, A., Rao, Y., and Huang, Y. (2018) Roles of albumin-binding proteins in cancer progression and biomimetic targeted drug delivery, ChemBioChem, 19, 1796-1805, https://doi.org/10.1002/cbic.201800201.

    Article  CAS  PubMed  Google Scholar 

  41. Thelu, H. V. P., Atchimnaidu, S., Perumal, D., Harikrishnan, K. S., Vijayan, S., and Varghese, R. (2019) Self-assembly of an aptamer-decorated, DNA–protein hybrid nanogel: a biocompatible nanocarrier for targeted cancer therapy, ACS Appl. Bio Mater., 2, 5227-5234, https://doi.org/10.1021/acsabm.9b00323.

    Article  CAS  PubMed  Google Scholar 

  42. Huang, J., Ma, W., Sun, H., Wang, H., He, X., Cheng, H., Huang, M., Lei, Y., and Wang, K. (2020) Self-assembled DNA nanostructures-based nanocarriers enabled functional nucleic acids delivery, ACS Appl. Bio Mater., 3, 2779-2795, https://doi.org/10.1021/acsabm.9b01197.

    Article  CAS  PubMed  Google Scholar 

  43. Harris, M. A., Kuang, H., Schneiderman, Z., Shiao, M. L., Crane, A. T., Chrostek, M. R., Tăbăran, A.-F., Pengo, T., Liaw, K., Xu, B., Lin, L., Chen, C. C., O’Sullivan, M. G., Kannan, R., Low, W. C., and Kokkoli, E. (2021) ssDNA nanotubes for selective targeting of glioblastoma and delivery of doxorubicin for enhanced survival, Sci. Adv., 7, eabl5872, https://doi.org/10.1126/sciadv.abl5872.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Liu, J., Chen, L., Zhai, T., Li, W., Liu, Y., and Gu, H. (2022) Programmable assembly of amphiphilic DNA through controlled cholesterol stacking, J. Am. Chem. Soc., 144, 16598-16603, https://doi.org/10.1021/jacs.2c06610.

    Article  CAS  PubMed  Google Scholar 

  45. Ma, W., Zhan, Y., Zhang, Y., Mao, C., Xie, X., and Lin, Y. (2021) The biological applications of DNA nanomaterials: current challenges and future directions, Signal Transduct. Target. Ther., 6, 351, https://doi.org/10.1038/s41392-021-00727-9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Li, J., Zheng, C., Cansiz, S., Wu, C., Xu, J., Cui, C., Liu, Y., Hou, W., Wang, Y., Zhang, L., Teng, I-T., Yang, H.-H., and Tan, W. (2015) Self-assembly of DNA nanohydrogels with controllable size and stimuli-responsive property for targeted gene therapy, J. Am. Chem. Soc., 137, 1412-1415, https://doi.org/10.1021/ja512293f.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Raniolo, S., Unida, V., Vindigni, G., Stolfi, C., Iacovelli, F., Desideri, A., and Biocca, S. (2021) Combined and selective miR-21 silencing and doxorubicin delivery in cancer cells using tailored DNA nanostructures, Cell Death Dis., 12, 7, https://doi.org/10.1038/s41419-020-03339-3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Wang, Y., Cheng, J., Zhao, D., Liu, Y., Luo, T., Zhong, Y.-F., Mo, F., Kong, X.-Y., and Song, J. (2020) Designed DNA nanostructure grafted with erlotinib for non-small-cell lung cancer therapy, Nanoscale, 12, 23953, https://doi.org/10.1039/d0nr06945k.

    Article  CAS  PubMed  Google Scholar 

  49. Wang, H., Xiao, H., Zhu, X., Liu, Y., Fu, Z., Li, C., Lu, C., and Yang, H. (2021) A cyanine-mediated self-assembly system for the construction of a two-in-one nanodrug, Angew. Chem. Int. Ed., 60, 21226-21230, https://doi.org/10.1002/anie.202108393.

    Article  CAS  Google Scholar 

  50. Markov, O. V., Filatov, A. V., Kupryushkin, M. S., Chernikov, I. V., Patutina, O. A., Strunov, A. A., Chernolovskaya, E. L., Vlassov, V. V., Pyshnyi, D. V., and Zenkova, M. A. (2020) Transport oligonucleotides – a novel system for intracellular delivery of antisense therapeutics, Molecules, 25, 3663, https://doi.org/10.3390/molecules25163663.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Pavlova, A. S., Dovydenko, I. S., Kupryushkin, M. S., Grigor’eva, A. E., Pyshnaya, I. A., and Pyshnyi, D. V. (2020) Amphiphilic “like-a-brush” oligonucleotide conjugates with three dodecyl chains: self-assembly features of novel scaffold compounds for nucleic acids delivery, Nanomaterials, 10, 1948, https://doi.org/10.3390/nano10101948.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Fasano, M., Curry, S., Terreno, E., Galliano, M., Fanali, G., Narciso, P., Notari, S., and Ascenzi, P. (2005) The extraordinary ligand binding properties of human serum albumin, IUBMB Life, 57, 787-796, https://doi.org/10.1080/15216540500404093.

    Article  CAS  PubMed  Google Scholar 

  53. Fanali, G., di Masi, A., Trezza, V., Marino, M., Fasano, M., and Ascenzi, P. (2012) Human serum albumin: from bench to bedside, Mol. Aspects Med., 33, 209-290, https://doi.org/10.1016/j.mam.2011.12.002.

    Article  CAS  PubMed  Google Scholar 

  54. Knudsen Sand, K. M., Bern, M., Nilsen, J., Noordzij, H. T., Sandlie, I., and Andersen, J. T. (2015) Unraveling the interaction between FcRn and albumin: opportunities for design of albumin-based therapeutics, Front. Immunol., 5, 682, https://doi.org/10.3389/fimmu.2014.00682.

    Article  CAS  Google Scholar 

  55. Kupryushkin, M. S., Nekrasov, M. D., Stetsenko, D. A., and Pyshnyi, D. V. (2014) Efficient functionalization of oligonucleotides by new achiral nonnucleosidic monomers, Org. Lett., 16, 2842-2845, https://doi.org/10.1021/ol500668n.

    Article  CAS  PubMed  Google Scholar 

  56. Dunn, D. B., and Hall, R. H. (1975) Purines, pyrimidines, nucleosides and nucleotides: physical constants and spectral properties, in Handbook of Biochemistry and Molecular Biology (Fasman, G. D., eds) CRC Press, Cleveland, Vol. 1, pp. 65-215.

  57. Dobrynin, S., Kutseikin, S., Morozov, D., Krumkacheva, O., Spitsyna, A., Gatilov, Y., Silnikov, V., Angelovski, G., Bowman, M. K., Kirilyuk, I., and Chubarov, A. (2020) Human serum albumin labelled with sterically-hindered nitroxides as potential MRI CONTRAST Agents, Molecules, 25, 1709, https://doi.org/10.3390/molecules25071709.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Chubarov, A., Spitsyna, A., Krumkacheva, O., Mitin, D., Suvorov, D., Tormyshev, V., Fedin, M., Bowman, M. K., and Bagryanskaya, E. (2021) Reversible dimerization of human serum albumin, Molecules, 26, 108, https://doi.org/10.3390/molecules26010108.

    Article  CAS  Google Scholar 

  59. Atmeh, R. F., Arafa, I. M., and Al-Khateeb, M. (2007) Albumin aggregates: hydrodynamic shape and physico-chemical properties, Jordan J. Chem., 2, 169-182.

    CAS  Google Scholar 

  60. Owczarzy, R., Tataurov, A. V., Wu, Y., Manthey, J. A., McQuisten, K. A., Almabrazi, H. G., Pedersen, K. F., Lin, Y., Garretson, J., McEntaggart, N. O., Sailor, C. A., Dawson, R. B., and Peek, A. S. (2008) IDT SciTools: a suite for analysis and design of nucleic acid oligomers, Nucleic Acids Res., 36, W163-W169, https://doi.org/10.1093/nar/gkn198.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Alinovskaya, L. I., Sedykh, S. E., Ivanisenko, N. V., Soboleva, S. E., and Nevinsky, G. A. (2018) How human serum albumin recognizes DNA and RNA, Biol. Chem., 399, 347-360, https://doi.org/10.1515/hsz-2017-0243.

    Article  CAS  PubMed  Google Scholar 

  62. Bar-Ziv, R., and Libchaber, A. (2001) Effects of DNA sequence and structure on binding of RecA to single-stranded DNA, Proc. Natl. Acad. Sci. USA, 98, 9068-9073, https://doi.org/10.1073/pnas.15124289.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Fredrickson, D. S., and Gordon, R. S. (1958) The metabolism of albumin-bound C14-labeled unesterified fatty acids in normal human subjects, J. Clin. Invest., 37, 1504-1515, https://doi.org/10.1172/JCI103742.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Peters, Jr., T. (1995) All about Albumin. Biochemistry, Genetics, and Medical Applications, Academic Press, San Diego, https://doi.org/10.1016/B978-0-12-552110-9.X5000-4.

  65. Bhattacharya, A. A., Grüne, T., and Curry, S. (2000) Crystallographic analysis reveals common modes of binding of medium and long-chain fatty acids to human serum albumin, J. Mol. Biol., 303, 721-732, https://doi.org/10.1006/jmbi.2000.4158.

    Article  CAS  PubMed  Google Scholar 

  66. Curry, S. (2003) Plasma albumin as a fatty acid carrier, in Advances in Molecular and Cell Biology, Lipobiology (van der Vusse, G. J., eds) Elsevier, vol. 33, pp. 29-46.

  67. Fujiwara, S.-i., and Amisaki, T. (2008) Identification of high affinity fatty acid binding sites on human serum albumin by MM-PBSA method, Biophys. J., 94, 95-103, https://doi.org/10.1529/biophysj.107.111377.

    Article  CAS  PubMed  Google Scholar 

  68. Van der Vusse, G. J. (2009) Albumin as fatty acid transporter, Drug Metab. Pharmacokinet., 24, 300-307, https://doi.org/10.2133/dmpk.24.300.

    Article  CAS  PubMed  Google Scholar 

  69. Ascenzi, P., Bocedi, A., Notari, S., Fanali, G., Fesce, R., and Fasano, M. (2006) Allosteric modulation of drug binding to human serum albumin, Mini. Rev. Med. Chem., 6, 483-489, https://doi.org/10.2174/138955706776361448.

    Article  CAS  PubMed  Google Scholar 

  70. Agudelo, D., Bourassa, P., Bruneau, J., Bérubé, G., Asselin, É., and Tajmir-Riahi, H.-A. (2012) Probing the binding sites of antibiotic drugs doxorubicin and N-(trifluoroacetyl) doxorubicin with human and bovine serum albumins, PLoS One, 7, e43814, https://doi.org/10.1371/journal.pone.0043814.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Golianová, K., Havadej, S., Verebová, V., Uličný, J., Holečková, B., and Staničová, J. (2021) Interaction of conazole pesticides epoxiconazole and prothioconazole with human and bovine serum albumin studied using spectroscopic methods and molecular modeling, Int. J. Mol. Sci., 22, 1925, https://doi.org/10.3390/ijms22041925.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Bisker, G., Ahn, J., Kruss, S., Ulissi, Z. W., Salem, D. P., and Strano, M. S. (2015) A mathematical formulation and solution of the CoPhMoRe inverse problem for helically wrapping polymer corona phases on cylindrical substrates, J. Phys. Chem. C, 119, 13876-13886, https://doi.org/10.1021/acs.jpcc.5b01705.

    Article  CAS  Google Scholar 

  73. Beckwitt, E., Kong, M., and Van Houten, B. (2018) Studying protein–DNA interactions using atomic force microscopy, Semin. Cell Dev. Biol., 73, 220-230, https://doi.org/10.1016/j.semcdb.2017.06.028.

    Article  CAS  PubMed  Google Scholar 

  74. Pyshnaya, I. A., Pyshnyi, D. V., Lomzov, A. A., Zarytova, V. F., and Ivanova, E. M. (2004) The influence of the non-nucleotide insert on the hybridization properties of oligonucleotides, Nucleosides Nucleotides Nucleic Acids, 23, 1065-1071, https://doi.org/10.1081/NCN-200026073.

    Article  CAS  PubMed  Google Scholar 

  75. Vinogradova, O. A., Eremeeva, E. V., Lomzov, A. A., Pyshnaya, I. A., and Pyshnyi, D. V. (2009) Bent dsDNA with defined geometric characteristics in terms of complexes of bridged oligonucleotides, Russ. J. Bioorg. Chem., 35, 349-359, https://doi.org/10.1134/S1068162009030108.

    Article  CAS  Google Scholar 

  76. Vinogradova, O. A., Scheglov, D. V., Latyshev, A. V., and Pyshnyi, D. V. (2011) Study of the structural organization of concatemeric complexes based on native and modified dsDNA blocks [in Russian], Vestnik NGU Ser. Biol. Clin. Med., 9, 109-117.

    Google Scholar 

  77. Pyne, A. L. B., Noy, A., Main, K. H. S., Velasco-Berrelleza, V., Piperakis, M. M., Mitchenall, L. A., Cugliandolo, F. M., Beton, J. G., Stevenson, C. E. M., Hoogenboom, B. W., Bates, A. D., Maxwell, A., and Harris, S. A. (2021) Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides, Nat. Commun., 12, 1053, https://doi.org/10.1038/s41467-021-21243-y.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Zhang, W., and Tung, C.-H. (2017) Sequence-independent DNA nanogel as a potential drug carrier, Macromol. Rapid Commun., 38, 1700366, https://doi.org/10.1002/marc.201700366.

    Article  CAS  Google Scholar 

  79. Lacroix, A., Edwardson, T. G. W., Hancock, M. A., Dore, M. D., and Sleiman, H. F. (2017) Development of DNA nanostructures for high-affinity binding to human serum albumin, J. Am. Chem. Soc., 139, 7355-7362, https://doi.org/10.1021/jacs.7b02917.

    Article  CAS  PubMed  Google Scholar 

  80. Arabi, S. H., Aghelnejad, B., Schwieger, C., Meister, A., Kerth, A., and Hinderberger, D. (2018) Serum albumin hydrogels in broad pH and temperature ranges: characterization of their self-assembled structures and nanoscopic and macroscopic properties, Biomater. Sci., 6, 478, https://doi.org/10.1039/c7bm00820a.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

A.S.P. expresses her gratitude to Dr. A. A. Lomzov and Dr. V. M. Golyshev (Laboratory of Structural Biology, ICBFM, SB RAS) for their invaluable help with AFM. VersaDoc™ MP 4000 Molecular Imager® System (Bio-Rad Laboratories, USA) from the Genomic Core Facility, ICBFM, SB RAS was used in the work.

Funding

This work was financially supported by the Russian State-funded project for the Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM, SB RAS) (grant number 121031300042-1).

Author information

Authors and Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia

    Anna S. Pavlova, Valeriya V. Ilyushchenko, Maxim S. Kupryushkin, Timofey D. Zharkov, Evgeniya S. Dyudeeva, Irina A. Bauer, Alexey S. Chubarov, Dmitrii V. Pyshnyi & Inna A. Pyshnaya

Authors
  1. Anna S. Pavlova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Valeriya V. Ilyushchenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maxim S. Kupryushkin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Timofey D. Zharkov
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Evgeniya S. Dyudeeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Irina A. Bauer
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Alexey S. Chubarov
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Dmitrii V. Pyshnyi
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Inna A. Pyshnaya
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

A.S.P. concept of the study, post-synthetic isolation of DCO, conducting experiments (electrophoretic mobility shift assay, AFM), processing and analysis of the obtained data, writing text of the paper; V.V.I. conducting experiments (electrophoretic mobility shift assay in PAAG), analysis and processing of the primary data; T.D.Zh., M.S.K., E.S.D. synthesis and post-synthetic isolation DCO and control oligonucleotides; I.A.B., A.S.Ch. isolation and purification of the HSA monomeric fraction; D.V.P., I.A.P. concept and supervision of the work, editing the text of the paper.

Corresponding authors

Correspondence to Anna S. Pavlova or Inna A. Pyshnaya.

Ethics declarations

The authors declare no conflict of interests in financial or any other sphere. This article does not contain any studies with human participants or animals performed by any of the authors.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Pavlova, A.S., Ilyushchenko, V.V., Kupryushkin, M.S. et al. Complexes and Supramolecular Associates of Dodecyl-Containing Oligonucleotides with Serum Albumin. Biochemistry Moscow 88, 1165–1180 (2023). https://doi.org/10.1134/S0006297923080102

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0006297923080102

Keywords

Search

Navigation