Araştırma Makalesi
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Yıl 2021, Cilt 5, Sayı 1, 13 - 19, 15.06.2021
https://doi.org/10.33435/tcandtc.828634

Öz

Kaynakça

  • Watson JD, Crick FH. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature. 1953;171:737-8.
  • Watson JD, Crick FH. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature. 1953;171:737-8.
  • Shu JJ. A new integrated symmetrical table for genetic codes. Biosystems. 2017;151:21-6.
  • Shu JJ. A new integrated symmetrical table for genetic codes. Biosystems. 2017;151:21-6.
  • Tan SC, Yiap BC. DNA, RNA, and protein extraction: the past and the present. Journal of Biomedicine and Biotechnology. 2009;2009:574398.
  • Tan SC, Yiap BC. DNA, RNA, and protein extraction: the past and the present. Journal of Biomedicine and Biotechnology. 2009;2009:574398.
  • Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C. A new and updated resource for codon usage tables. BMC Bioinformatics. 2017;18:1-0.
  • Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C. A new and updated resource for codon usage tables. BMC Bioinformatics. 2017;18:1-0.
  • Simmons MP. Relative benefits of amino‐acid, codon, degeneracy, DNA, and purine‐pyrimidine character coding for phylogenetic analyses of exons. Journal of Systematics and Evolution. 2017;55:85-109.
  • Simmons MP. Relative benefits of amino‐acid, codon, degeneracy, DNA, and purine‐pyrimidine character coding for phylogenetic analyses of exons. Journal of Systematics and Evolution. 2017;55:85-109.
  • Stein CK, Pawlyn C, Chavan S, Rasche L, Weinhold N, Corken A, Buros A, Sonneveld P, Jackson GH, Landgren O, Mughal T. The varied distribution and impact of RAS codon and other key DNA alterations across the translocation cyclin D subgroups in multiple myeloma. Oncotarget. 2017;8:27854.
  • Stein CK, Pawlyn C, Chavan S, Rasche L, Weinhold N, Corken A, Buros A, Sonneveld P, Jackson GH, Landgren O, Mughal T. The varied distribution and impact of RAS codon and other key DNA alterations across the translocation cyclin D subgroups in multiple myeloma. Oncotarget. 2017;8:27854.
  • Rapino F, Delaunay S, Rambow F, Zhou Z, Tharun L, De Tullio P, Sin O, Shostak K, Schmitz S, Piepers J, Ghesquière B. Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature. 2018;558:605-9.
  • Rapino F, Delaunay S, Rambow F, Zhou Z, Tharun L, De Tullio P, Sin O, Shostak K, Schmitz S, Piepers J, Ghesquière B. Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature. 2018;558:605-9.
  • Crick FH, Barnett L, Brenner S, Watts-Tobin RJ. General nature of the genetic code for proteins. Nature. 1961;192:1227-32.
  • Crick FH, Barnett L, Brenner S, Watts-Tobin RJ. General nature of the genetic code for proteins. Nature. 1961;192:1227-32.
  • Karlin S, Mrázek J. What drives codon choices in human genes?. Journal of Molecular Biology. 1996;262:459-72.
  • Karlin S, Mrázek J. What drives codon choices in human genes?. Journal of Molecular Biology. 1996;262:459-72.
  • Alexaki A, Kames J, Holcomb DD, Athey J, Santana-Quintero LV, Lam PV, Hamasaki-Katagiri N, Osipova E, Simonyan V, Bar H, Komar AA. Codon and codon-pair usage tables (CoCoPUTs): facilitating genetic variation analyses and recombinant gene design. Journal of Molecular Biology. 2019;431:2434-41.
  • Alexaki A, Kames J, Holcomb DD, Athey J, Santana-Quintero LV, Lam PV, Hamasaki-Katagiri N, Osipova E, Simonyan V, Bar H, Komar AA. Codon and codon-pair usage tables (CoCoPUTs): facilitating genetic variation analyses and recombinant gene design. Journal of Molecular Biology. 2019;431:2434-41.
  • Groenke N, Trimpert J, Merz S, Conradie AM, Wyler E, Zhang H, Hazapis OG, Rausch S, Landthaler M, Osterrieder N, Kunec D. Mechanism of virus attenuation by codon pair deoptimization. Cell Reports. 2020;31:107586.
  • Groenke N, Trimpert J, Merz S, Conradie AM, Wyler E, Zhang H, Hazapis OG, Rausch S, Landthaler M, Osterrieder N, Kunec D. Mechanism of virus attenuation by codon pair deoptimization. Cell Reports. 2020;31:107586.
  • Dilucca M, Forcelloni S, Georgakilas AG, Giansanti A, Pavlopoulou A. Codon usage and phenotypic divergences of SARS-CoV-2 genes. Viruses. 2020;12:498.
  • Dilucca M, Forcelloni S, Georgakilas AG, Giansanti A, Pavlopoulou A. Codon usage and phenotypic divergences of SARS-CoV-2 genes. Viruses. 2020;12:498.
  • Lopes A, Vanvarenberg K, Préat V, Vandermeulen G. Codon-optimized P1A-encoding DNA vaccine: toward a therapeutic vaccination against P815 mastocytoma. Molecular Therapy-Nucleic Acids. 2017;8:404-15.
  • Lopes A, Vanvarenberg K, Préat V, Vandermeulen G. Codon-optimized P1A-encoding DNA vaccine: toward a therapeutic vaccination against P815 mastocytoma. Molecular Therapy-Nucleic Acids. 2017;8:404-15.
  • Iijima S. Carbon nanotubes: past, present, and future. Physica B. 2002;323:1-5.
  • Iijima S. Carbon nanotubes: past, present, and future. Physica B. 2002;323:1-5.
  • Mirzaei M, Kalhor HR, Hadipour NL. Covalent hybridization of CNT by thymine and uracil: A computational study. Journal of Molecular Modeling. 2011;17:695-9.
  • Mirzaei M, Kalhor HR, Hadipour NL. Covalent hybridization of CNT by thymine and uracil: A computational study. Journal of Molecular Modeling. 2011;17:695-9.
  • Mirzaei M, Yousefi M. Computational studies of the purine-functionalized graphene sheets. Superlattices and Microstructures. 2012;52:612-7.
  • Mirzaei M, Yousefi M. Computational studies of the purine-functionalized graphene sheets. Superlattices and Microstructures. 2012;52:612-7.
  • Pagar T, Ghotekar S, Pansambal S, Pagar K, Oza R. Biomimetic synthesis of CuO nanoparticle using Capparis decidua and their antibacterial activity. Advanced Journal of Science and Engineering. 2020;1:133-7.
  • Pagar T, Ghotekar S, Pansambal S, Pagar K, Oza R. Biomimetic synthesis of CuO nanoparticle using Capparis decidua and their antibacterial activity. Advanced Journal of Science and Engineering. 2020;1:133-7.
  • Faramarzi R, Falahati M, Mirzaei M. Interactions of fluorouracil by CNT and BNNT: DFT analyses. Advanced Journal of Science and Engineering. 2020;1:62-6.
  • Faramarzi R, Falahati M, Mirzaei M. Interactions of fluorouracil by CNT and BNNT: DFT analyses. Advanced Journal of Science and Engineering. 2020;1:62-6.
  • Mirzaei M. Effects of carbon nanotubes on properties of the fluorouracil anticancer drug: DFT studies of a CNT-fluorouracil compound. International Journal of Nano Dimension. 2013;3:175-9.
  • Mirzaei M. Effects of carbon nanotubes on properties of the fluorouracil anticancer drug: DFT studies of a CNT-fluorouracil compound. International Journal of Nano Dimension. 2013;3:175-9.
  • Eaton PE, Cole TW. Cubane. Journal of the American Chemical Society. 1964;86:3157-8.
  • Eaton PE, Cole TW. Cubane. Journal of the American Chemical Society. 1964;86:3157-8.
  • Biegasiewicz KF, Griffiths JR, Savage GP, Tsanaktsidis J, Priefer R. Cubane: 50 years later. Chemical Reviews. 2015;115:6719-45.
  • Biegasiewicz KF, Griffiths JR, Savage GP, Tsanaktsidis J, Priefer R. Cubane: 50 years later. Chemical Reviews. 2015;115:6719-45.
  • Bernhard SS, Locke GM, Plunkett S, Meindl A, Flanagan KJ, Senge MO. Cubane cross-coupling and cubane–porphyrin arrays. Chemistry - A European Journal. 2018;24:1026-30.
  • Bernhard SS, Locke GM, Plunkett S, Meindl A, Flanagan KJ, Senge MO. Cubane cross-coupling and cubane–porphyrin arrays. Chemistry - A European Journal. 2018;24:1026-30.
  • Deville C, Folkjær M, Reinholdt P, Hvid MS, Lamagni P, Borup K, Sun Z, Lauritsen JV, McKee V, Jensen KM, Lock N. Cubes on a string: A series of linear coordination polymers with cubane-like nodes and dicarboxylate linkers. Nanoscale. 2020;12:11601-11
  • Deville C, Folkjær M, Reinholdt P, Hvid MS, Lamagni P, Borup K, Sun Z, Lauritsen JV, McKee V, Jensen KM, Lock N. Cubes on a string: A series of linear coordination polymers with cubane-like nodes and dicarboxylate linkers. Nanoscale. 2020;12:11601-11
  • Mirzaei M. Science and engineering in silico. Advanced Journal of Science and Engineering. 2020;1:1-2.
  • Mirzaei M. Science and engineering in silico. Advanced Journal of Science and Engineering. 2020;1:1-2.
  • Froimowitz M. HyperChem: a software package for computational chemistry and molecular modeling. Biotechniques. 1993;14:1010-3.
  • Froimowitz M. HyperChem: a software package for computational chemistry and molecular modeling. Biotechniques. 1993;14:1010-3.
  • Frisch MJ et al., Gaussian 09, Revision D.01, Gaussian. Inc., Wallingford CT, 2013.
  • Frisch MJ et al., Gaussian 09, Revision D.01, Gaussian. Inc., Wallingford CT, 2013.
  • Yan Y, Zhang D, Zhou P, Li B, Huang SY. HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy. Nucleic Acids Research. 2017;45:365-73.
  • Yan Y, Zhang D, Zhou P, Li B, Huang SY. HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy. Nucleic Acids Research. 2017;45:365-73.
  • Behzadi H, Hadipour NL, Mirzaei M. A density functional study of 17O, 14N and 2H electric field gradient tensors in the real crystalline structure of α-glycine. Biophysical Chemistry. 2007;125:179-83.
  • Behzadi H, Hadipour NL, Mirzaei M. A density functional study of 17O, 14N and 2H electric field gradient tensors in the real crystalline structure of α-glycine. Biophysical Chemistry. 2007;125:179-83.
  • Mirzaei M, Hadipour NL, Abolhassani MR. Influence of C-doping on the B-11 and N-14 quadrupole coupling constants in boron-nitride nanotubes: A DFT study. Zeitschrift für Naturforschung A. 2007;62:56-60.
  • Mirzaei M, Hadipour NL, Abolhassani MR. Influence of C-doping on the B-11 and N-14 quadrupole coupling constants in boron-nitride nanotubes: A DFT study. Zeitschrift für Naturforschung A. 2007;62:56-60.
  • Samadi Z, Mirzaei M, Hadipour NL, Khorami SA. Density functional calculations of oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors to study hydrogen bonding properties of peptide group (OC–NH) in crystalline acetamide. Journal of Molecular Graphics and Modelling. 2008;26:977-81.
  • Samadi Z, Mirzaei M, Hadipour NL, Khorami SA. Density functional calculations of oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors to study hydrogen bonding properties of peptide group (OC–NH) in crystalline acetamide. Journal of Molecular Graphics and Modelling. 2008;26:977-81.
  • Farahbakhsh Z, Zamani MR, Rafienia M, Gulseren O, Mirzaei M. In silico activity of AS1411 aptamer against nucleolin of cancer cells. Iranian Journal of Blood and Cancer. 2020;12:95-10
  • Farahbakhsh Z, Zamani MR, Rafienia M, Gulseren O, Mirzaei M. In silico activity of AS1411 aptamer against nucleolin of cancer cells. Iranian Journal of Blood and Cancer. 2020;12:95-10

DNA Codon Recognition by a Cubane Wire: In Silico Approach

Yıl 2021, Cilt 5, Sayı 1, 13 - 19, 15.06.2021
https://doi.org/10.33435/tcandtc.828634

Öz

DNA codons, consisting of triplet nucleotides (NTs), could play important roles for RNA transcription and protein translation in living systems. Therefore, their recognition could be seen important for diagnosis and therapy purposes. Based on triplet sequence formations of Adenine (A), Guanine (G), Cytosine (C) and Thymine (T) NTs, 64 codons were investigated in this work regarding their complexation with a molecular cubane (CUB) wire. To achieve this aim, each of singular 64 codons and CUB were optimized to be prepared for docking processes of complex formations. Hence, 64 complexes of codon-CUB were docked to see the recognition potency of CUB wire versus each of DNA codons. Interestingly, the obtained docking scores indicated that the CUB could work specifically versus the DNA codons, in which G-rich and A-rich triples were seen to be more favorable for complexation with CUB in comparison with other C-rich and T-rich triplet codons. Moreover, the results indicated that not pure G triplet but GAG codon was the most favorable one to be recognized by the CUB wire. However, pure T triplet was the worst one for such complex formations. The results of this work remarkably indicated that the CUB wire could work for recognition process of DNA codons from each other and such recognition could be very much specified for each of G-rich and A-rich codons, in which GAG codon was the best one among all the 64 investigated codons.

Kaynakça

  • Watson JD, Crick FH. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature. 1953;171:737-8.
  • Watson JD, Crick FH. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature. 1953;171:737-8.
  • Shu JJ. A new integrated symmetrical table for genetic codes. Biosystems. 2017;151:21-6.
  • Shu JJ. A new integrated symmetrical table for genetic codes. Biosystems. 2017;151:21-6.
  • Tan SC, Yiap BC. DNA, RNA, and protein extraction: the past and the present. Journal of Biomedicine and Biotechnology. 2009;2009:574398.
  • Tan SC, Yiap BC. DNA, RNA, and protein extraction: the past and the present. Journal of Biomedicine and Biotechnology. 2009;2009:574398.
  • Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C. A new and updated resource for codon usage tables. BMC Bioinformatics. 2017;18:1-0.
  • Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C. A new and updated resource for codon usage tables. BMC Bioinformatics. 2017;18:1-0.
  • Simmons MP. Relative benefits of amino‐acid, codon, degeneracy, DNA, and purine‐pyrimidine character coding for phylogenetic analyses of exons. Journal of Systematics and Evolution. 2017;55:85-109.
  • Simmons MP. Relative benefits of amino‐acid, codon, degeneracy, DNA, and purine‐pyrimidine character coding for phylogenetic analyses of exons. Journal of Systematics and Evolution. 2017;55:85-109.
  • Stein CK, Pawlyn C, Chavan S, Rasche L, Weinhold N, Corken A, Buros A, Sonneveld P, Jackson GH, Landgren O, Mughal T. The varied distribution and impact of RAS codon and other key DNA alterations across the translocation cyclin D subgroups in multiple myeloma. Oncotarget. 2017;8:27854.
  • Stein CK, Pawlyn C, Chavan S, Rasche L, Weinhold N, Corken A, Buros A, Sonneveld P, Jackson GH, Landgren O, Mughal T. The varied distribution and impact of RAS codon and other key DNA alterations across the translocation cyclin D subgroups in multiple myeloma. Oncotarget. 2017;8:27854.
  • Rapino F, Delaunay S, Rambow F, Zhou Z, Tharun L, De Tullio P, Sin O, Shostak K, Schmitz S, Piepers J, Ghesquière B. Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature. 2018;558:605-9.
  • Rapino F, Delaunay S, Rambow F, Zhou Z, Tharun L, De Tullio P, Sin O, Shostak K, Schmitz S, Piepers J, Ghesquière B. Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature. 2018;558:605-9.
  • Crick FH, Barnett L, Brenner S, Watts-Tobin RJ. General nature of the genetic code for proteins. Nature. 1961;192:1227-32.
  • Crick FH, Barnett L, Brenner S, Watts-Tobin RJ. General nature of the genetic code for proteins. Nature. 1961;192:1227-32.
  • Karlin S, Mrázek J. What drives codon choices in human genes?. Journal of Molecular Biology. 1996;262:459-72.
  • Karlin S, Mrázek J. What drives codon choices in human genes?. Journal of Molecular Biology. 1996;262:459-72.
  • Alexaki A, Kames J, Holcomb DD, Athey J, Santana-Quintero LV, Lam PV, Hamasaki-Katagiri N, Osipova E, Simonyan V, Bar H, Komar AA. Codon and codon-pair usage tables (CoCoPUTs): facilitating genetic variation analyses and recombinant gene design. Journal of Molecular Biology. 2019;431:2434-41.
  • Alexaki A, Kames J, Holcomb DD, Athey J, Santana-Quintero LV, Lam PV, Hamasaki-Katagiri N, Osipova E, Simonyan V, Bar H, Komar AA. Codon and codon-pair usage tables (CoCoPUTs): facilitating genetic variation analyses and recombinant gene design. Journal of Molecular Biology. 2019;431:2434-41.
  • Groenke N, Trimpert J, Merz S, Conradie AM, Wyler E, Zhang H, Hazapis OG, Rausch S, Landthaler M, Osterrieder N, Kunec D. Mechanism of virus attenuation by codon pair deoptimization. Cell Reports. 2020;31:107586.
  • Groenke N, Trimpert J, Merz S, Conradie AM, Wyler E, Zhang H, Hazapis OG, Rausch S, Landthaler M, Osterrieder N, Kunec D. Mechanism of virus attenuation by codon pair deoptimization. Cell Reports. 2020;31:107586.
  • Dilucca M, Forcelloni S, Georgakilas AG, Giansanti A, Pavlopoulou A. Codon usage and phenotypic divergences of SARS-CoV-2 genes. Viruses. 2020;12:498.
  • Dilucca M, Forcelloni S, Georgakilas AG, Giansanti A, Pavlopoulou A. Codon usage and phenotypic divergences of SARS-CoV-2 genes. Viruses. 2020;12:498.
  • Lopes A, Vanvarenberg K, Préat V, Vandermeulen G. Codon-optimized P1A-encoding DNA vaccine: toward a therapeutic vaccination against P815 mastocytoma. Molecular Therapy-Nucleic Acids. 2017;8:404-15.
  • Lopes A, Vanvarenberg K, Préat V, Vandermeulen G. Codon-optimized P1A-encoding DNA vaccine: toward a therapeutic vaccination against P815 mastocytoma. Molecular Therapy-Nucleic Acids. 2017;8:404-15.
  • Iijima S. Carbon nanotubes: past, present, and future. Physica B. 2002;323:1-5.
  • Iijima S. Carbon nanotubes: past, present, and future. Physica B. 2002;323:1-5.
  • Mirzaei M, Kalhor HR, Hadipour NL. Covalent hybridization of CNT by thymine and uracil: A computational study. Journal of Molecular Modeling. 2011;17:695-9.
  • Mirzaei M, Kalhor HR, Hadipour NL. Covalent hybridization of CNT by thymine and uracil: A computational study. Journal of Molecular Modeling. 2011;17:695-9.
  • Mirzaei M, Yousefi M. Computational studies of the purine-functionalized graphene sheets. Superlattices and Microstructures. 2012;52:612-7.
  • Mirzaei M, Yousefi M. Computational studies of the purine-functionalized graphene sheets. Superlattices and Microstructures. 2012;52:612-7.
  • Pagar T, Ghotekar S, Pansambal S, Pagar K, Oza R. Biomimetic synthesis of CuO nanoparticle using Capparis decidua and their antibacterial activity. Advanced Journal of Science and Engineering. 2020;1:133-7.
  • Pagar T, Ghotekar S, Pansambal S, Pagar K, Oza R. Biomimetic synthesis of CuO nanoparticle using Capparis decidua and their antibacterial activity. Advanced Journal of Science and Engineering. 2020;1:133-7.
  • Faramarzi R, Falahati M, Mirzaei M. Interactions of fluorouracil by CNT and BNNT: DFT analyses. Advanced Journal of Science and Engineering. 2020;1:62-6.
  • Faramarzi R, Falahati M, Mirzaei M. Interactions of fluorouracil by CNT and BNNT: DFT analyses. Advanced Journal of Science and Engineering. 2020;1:62-6.
  • Mirzaei M. Effects of carbon nanotubes on properties of the fluorouracil anticancer drug: DFT studies of a CNT-fluorouracil compound. International Journal of Nano Dimension. 2013;3:175-9.
  • Mirzaei M. Effects of carbon nanotubes on properties of the fluorouracil anticancer drug: DFT studies of a CNT-fluorouracil compound. International Journal of Nano Dimension. 2013;3:175-9.
  • Eaton PE, Cole TW. Cubane. Journal of the American Chemical Society. 1964;86:3157-8.
  • Eaton PE, Cole TW. Cubane. Journal of the American Chemical Society. 1964;86:3157-8.
  • Biegasiewicz KF, Griffiths JR, Savage GP, Tsanaktsidis J, Priefer R. Cubane: 50 years later. Chemical Reviews. 2015;115:6719-45.
  • Biegasiewicz KF, Griffiths JR, Savage GP, Tsanaktsidis J, Priefer R. Cubane: 50 years later. Chemical Reviews. 2015;115:6719-45.
  • Bernhard SS, Locke GM, Plunkett S, Meindl A, Flanagan KJ, Senge MO. Cubane cross-coupling and cubane–porphyrin arrays. Chemistry - A European Journal. 2018;24:1026-30.
  • Bernhard SS, Locke GM, Plunkett S, Meindl A, Flanagan KJ, Senge MO. Cubane cross-coupling and cubane–porphyrin arrays. Chemistry - A European Journal. 2018;24:1026-30.
  • Deville C, Folkjær M, Reinholdt P, Hvid MS, Lamagni P, Borup K, Sun Z, Lauritsen JV, McKee V, Jensen KM, Lock N. Cubes on a string: A series of linear coordination polymers with cubane-like nodes and dicarboxylate linkers. Nanoscale. 2020;12:11601-11
  • Deville C, Folkjær M, Reinholdt P, Hvid MS, Lamagni P, Borup K, Sun Z, Lauritsen JV, McKee V, Jensen KM, Lock N. Cubes on a string: A series of linear coordination polymers with cubane-like nodes and dicarboxylate linkers. Nanoscale. 2020;12:11601-11
  • Mirzaei M. Science and engineering in silico. Advanced Journal of Science and Engineering. 2020;1:1-2.
  • Mirzaei M. Science and engineering in silico. Advanced Journal of Science and Engineering. 2020;1:1-2.
  • Froimowitz M. HyperChem: a software package for computational chemistry and molecular modeling. Biotechniques. 1993;14:1010-3.
  • Froimowitz M. HyperChem: a software package for computational chemistry and molecular modeling. Biotechniques. 1993;14:1010-3.
  • Frisch MJ et al., Gaussian 09, Revision D.01, Gaussian. Inc., Wallingford CT, 2013.
  • Frisch MJ et al., Gaussian 09, Revision D.01, Gaussian. Inc., Wallingford CT, 2013.
  • Yan Y, Zhang D, Zhou P, Li B, Huang SY. HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy. Nucleic Acids Research. 2017;45:365-73.
  • Yan Y, Zhang D, Zhou P, Li B, Huang SY. HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy. Nucleic Acids Research. 2017;45:365-73.
  • Behzadi H, Hadipour NL, Mirzaei M. A density functional study of 17O, 14N and 2H electric field gradient tensors in the real crystalline structure of α-glycine. Biophysical Chemistry. 2007;125:179-83.
  • Behzadi H, Hadipour NL, Mirzaei M. A density functional study of 17O, 14N and 2H electric field gradient tensors in the real crystalline structure of α-glycine. Biophysical Chemistry. 2007;125:179-83.
  • Mirzaei M, Hadipour NL, Abolhassani MR. Influence of C-doping on the B-11 and N-14 quadrupole coupling constants in boron-nitride nanotubes: A DFT study. Zeitschrift für Naturforschung A. 2007;62:56-60.
  • Mirzaei M, Hadipour NL, Abolhassani MR. Influence of C-doping on the B-11 and N-14 quadrupole coupling constants in boron-nitride nanotubes: A DFT study. Zeitschrift für Naturforschung A. 2007;62:56-60.
  • Samadi Z, Mirzaei M, Hadipour NL, Khorami SA. Density functional calculations of oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors to study hydrogen bonding properties of peptide group (OC–NH) in crystalline acetamide. Journal of Molecular Graphics and Modelling. 2008;26:977-81.
  • Samadi Z, Mirzaei M, Hadipour NL, Khorami SA. Density functional calculations of oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors to study hydrogen bonding properties of peptide group (OC–NH) in crystalline acetamide. Journal of Molecular Graphics and Modelling. 2008;26:977-81.
  • Farahbakhsh Z, Zamani MR, Rafienia M, Gulseren O, Mirzaei M. In silico activity of AS1411 aptamer against nucleolin of cancer cells. Iranian Journal of Blood and Cancer. 2020;12:95-10
  • Farahbakhsh Z, Zamani MR, Rafienia M, Gulseren O, Mirzaei M. In silico activity of AS1411 aptamer against nucleolin of cancer cells. Iranian Journal of Blood and Cancer. 2020;12:95-10

Ayrıntılar

Birincil Dil İngilizce
Konular Mühendislik, Kimya
Bölüm Research Article
Yazarlar

Mahmoud MIRZAEI (Sorumlu Yazar)
Isfahan University of Medical Sciences
0000-0001-9346-4901
Iran


Nasser HADİPOUR Bu kişi benim
Tarbiat Modares University
0000-0002-6759-6043
Iran


Oguz GULSEREN
İHSAN DOĞRAMACI BİLKENT ÜNİVERSİTESİ
0000-0002-7632-0954
Türkiye

Destekleyen Kurum Isfahan University of Medical Sciences
Proje Numarası 294218
Teşekkür The support of this work by the research council of Isfahan University of Medical Sciences under grant number 294218 is acknowledged.
Yayımlanma Tarihi 15 Haziran 2021
Başvuru Tarihi 20 Kasım 2020
Kabul Tarihi 11 Aralık 2020
Yayınlandığı Sayı Yıl 2021, Cilt 5, Sayı 1

Kaynak Göster

Bibtex @araştırma makalesi { tcandtc828634, journal = {Turkish Computational and Theoretical Chemistry}, issn = {2587-1722}, eissn = {2602-3237}, address = {}, publisher = {Koray SAYIN}, year = {2021}, volume = {5}, pages = {13 - 19}, doi = {10.33435/tcandtc.828634}, title = {DNA Codon Recognition by a Cubane Wire: In Silico Approach}, key = {cite}, author = {Mırzaeı, Mahmoud and Hadipour, Nasser and Gulseren, Oguz} }
APA Mırzaeı, M. , Hadipour, N. & Gulseren, O. (2021). DNA Codon Recognition by a Cubane Wire: In Silico Approach . Turkish Computational and Theoretical Chemistry , 5 (1) , 13-19 . DOI: 10.33435/tcandtc.828634
MLA Mırzaeı, M. , Hadipour, N. , Gulseren, O. "DNA Codon Recognition by a Cubane Wire: In Silico Approach" . Turkish Computational and Theoretical Chemistry 5 (2021 ): 13-19 <https://dergipark.org.tr/tr/pub/tcandtc/issue/60170/828634>
Chicago Mırzaeı, M. , Hadipour, N. , Gulseren, O. "DNA Codon Recognition by a Cubane Wire: In Silico Approach". Turkish Computational and Theoretical Chemistry 5 (2021 ): 13-19
RIS TY - JOUR T1 - DNA Codon Recognition by a Cubane Wire: In Silico Approach AU - Mahmoud Mırzaeı , Nasser Hadipour , Oguz Gulseren Y1 - 2021 PY - 2021 N1 - doi: 10.33435/tcandtc.828634 DO - 10.33435/tcandtc.828634 T2 - Turkish Computational and Theoretical Chemistry JF - Journal JO - JOR SP - 13 EP - 19 VL - 5 IS - 1 SN - 2587-1722-2602-3237 M3 - doi: 10.33435/tcandtc.828634 UR - https://doi.org/10.33435/tcandtc.828634 Y2 - 2020 ER -
EndNote %0 Turkish Computational and Theoretical Chemistry DNA Codon Recognition by a Cubane Wire: In Silico Approach %A Mahmoud Mırzaeı , Nasser Hadipour , Oguz Gulseren %T DNA Codon Recognition by a Cubane Wire: In Silico Approach %D 2021 %J Turkish Computational and Theoretical Chemistry %P 2587-1722-2602-3237 %V 5 %N 1 %R doi: 10.33435/tcandtc.828634 %U 10.33435/tcandtc.828634
ISNAD Mırzaeı, Mahmoud , Hadipour, Nasser , Gulseren, Oguz . "DNA Codon Recognition by a Cubane Wire: In Silico Approach". Turkish Computational and Theoretical Chemistry 5 / 1 (Haziran 2021): 13-19 . https://doi.org/10.33435/tcandtc.828634
AMA Mırzaeı M. , Hadipour N. , Gulseren O. DNA Codon Recognition by a Cubane Wire: In Silico Approach. Turkish Comp Theo Chem (TC&TC). 2021; 5(1): 13-19.
Vancouver Mırzaeı M. , Hadipour N. , Gulseren O. DNA Codon Recognition by a Cubane Wire: In Silico Approach. Turkish Computational and Theoretical Chemistry. 2021; 5(1): 13-19.
IEEE M. Mırzaeı , N. Hadipour ve O. Gulseren , "DNA Codon Recognition by a Cubane Wire: In Silico Approach", Turkish Computational and Theoretical Chemistry, c. 5, sayı. 1, ss. 13-19, Haz. 2021, doi:10.33435/tcandtc.828634

Journal Full Title: Turkish Computational and Theoretical Chemistry


Journal Abbreviated Title: Turkish Comp Theo Chem (TC&TC)