Research Article
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DNA Codon Recognition by a Cubane Wire: In Silico Approach

Year 2021, , 13 - 19, 15.06.2021

Mahmoud Mırzaeı , Nasser Hadipour Oguz Gulseren

https://doi.org/10.33435/tcandtc.828634
Cited By: 15

Abstract

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.

Keywords

Codon DNA Triplet Cubane In silico

Supporting Institution

Isfahan University of Medical Sciences

Project Number

294218

Thanks

The support of this work by the research council of Isfahan University of Medical Sciences under grant number 294218 is acknowledged.

References

  • 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

Year 2021, , 13 - 19, 15.06.2021

Mahmoud Mırzaeı , Nasser Hadipour Oguz Gulseren

https://doi.org/10.33435/tcandtc.828634
Cited By: 15

Abstract

Project Number

294218

References

  • 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
There are 62 citations in total.

Details

Primary Language English
Subjects Chemical Engineering
Journal Section Research Article
Authors

Mahmoud Mırzaeı 0000-0001-9346-4901

Nasser Hadipour This is me 0000-0002-6759-6043

Oguz Gulseren 0000-0002-7632-0954

Project Number 294218
Publication Date June 15, 2021
Submission Date November 20, 2020
Published in Issue Year 2021

Cite

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. 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). June 2021;5(1):13-19. doi:10.33435/tcandtc.828634
Chicago Mırzaeı, Mahmoud, Nasser Hadipour, and Oguz Gulseren. “DNA Codon Recognition by a Cubane Wire: In Silico Approach”. Turkish Computational and Theoretical Chemistry 5, no. 1 (June 2021): 13-19. https://doi.org/10.33435/tcandtc.828634.
EndNote Mırzaeı M, Hadipour N, Gulseren O (June 1, 2021) DNA Codon Recognition by a Cubane Wire: In Silico Approach. Turkish Computational and Theoretical Chemistry 5 1 13–19.
IEEE M. Mırzaeı, N. Hadipour, and O. Gulseren, “DNA Codon Recognition by a Cubane Wire: In Silico Approach”, Turkish Comp Theo Chem (TC&TC), vol. 5, no. 1, pp. 13–19, 2021, doi: 10.33435/tcandtc.828634.
ISNAD Mırzaeı, Mahmoud et al. “DNA Codon Recognition by a Cubane Wire: In Silico Approach”. Turkish Computational and Theoretical Chemistry 5/1 (June 2021), 13-19. https://doi.org/10.33435/tcandtc.828634.
JAMA Mırzaeı M, Hadipour N, Gulseren O. DNA Codon Recognition by a Cubane Wire: In Silico Approach. Turkish Comp Theo Chem (TC&TC). 2021;5:13–19.
MLA Mırzaeı, Mahmoud et al. “DNA Codon Recognition by a Cubane Wire: In Silico Approach”. Turkish Computational and Theoretical Chemistry, vol. 5, no. 1, 2021, pp. 13-19, doi:10.33435/tcandtc.828634.
Vancouver 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):13-9.

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Molecularly imprinted polymer-based sensors for identification volatile compounds in pharmaceutical products: in silico rational design
Journal of Biomolecular Structure and Dynamics
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A C19Ti Cage vehicle for the drug delivery of purinethol Anticancer: Computational assessments
Computational and Theoretical Chemistry
https://doi.org/10.1016/j.comptc.2022.113760
Exploring curcumin interactions with BN nanostructures: A DFT approach
Main Group Chemistry
https://doi.org/10.3233/MGC-210151
Iron Chelation by thiocytosine: Investigating electronic and structural features for describing tautomerism and metal chelation processes
Main Group Chemistry
https://doi.org/10.3233/MGC-210110
Investigating thiouracil adsorption by an iron-doped carbon particle: Analyzing structural, electronic, and QTAIM features
Journal of Molecular Structure
https://doi.org/10.1016/j.molstruc.2021.131885
Structural analysis of an iron-assisted carbon monolayer for delivery of 2-thiouracil
Main Group Chemistry
https://doi.org/10.3233/MGC-210079
Formations of bimolecular barbituric acid complexes through hydrogen bonding interactions: DFT analyses of structural and electronic features
Main Group Chemistry
https://doi.org/10.3233/MGC-210102
Interaction of a conical carbon scaffold with the thio-substituted model of fluorouracil towards approaching the drug delivery purposes
Main Group Chemistry
https://doi.org/10.3233/MGC-210174
4-Amino modified derivatives of cytidine towards interactions with the methyltransferase enzyme
Main Group Chemistry
https://doi.org/10.3233/MGC-210185
Electronic and structural computing features of some chromene derivatives and evaluating their anticancer activities
Main Group Chemistry
https://doi.org/10.3233/MGC-210136
Interactions between favipiravir and a BNC cage towards drug delivery applications
Structural Chemistry
https://doi.org/10.1007/s11224-021-01833-8
Double chelation of Iron through dimer formation of favipiravir: Density functional theory analysis
Main Group Chemistry
https://doi.org/10.3233/MGC-210182
Simulating a heteroatomic CBN fullerene-like nanocage towards the drug delivery of fluorouracil
Molecular Simulation
https://doi.org/10.1080/08927022.2022.2086252
A quick review of advantages and limitations of biological fertilizers in wheat cultivation
Main Group Chemistry
https://doi.org/10.3233/MGC-210171
Affinity variation in the interactions of tryptophan- β-cyclodextrin-platinum complex with G-quadruplex and duplex DNAs
Journal of Biomolecular Structure and Dynamics
https://doi.org/10.1080/07391102.2022.2090440

Journal Full Title: Turkish Computational and Theoretical Chemistry


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