此研究使用分子動力學模擬賴氨酸轉移核醣核酸(tRNALys,3)並且使用GROMOS 96來當作模擬的勢能，初始的轉移核醣核酸擁有位置34的mcm5s2U34的核酸修飾與位置37的ms2t6A37核酸修飾。而在整體的模擬時間，我們設定500微微秒(ps)當作我們模擬的總時間，其整體系統加入鈉(Na+)離子來中和整體系統的電性，使其成為電中性的系統，而且結果也顯示出tRNALys,3分子的穩定性，分析轉移核醣核酸的均分根誤差值發現由76個核苷酸構成的初始轉移核醣核酸，其L結構的外型呈現穩定的構形。其結構機制會呈現穩定構形，主要是因為大多數的鹼基產生氫鍵作用。氫鍵於第三類鹼基是薄弱的，因此不會產生任何的穩定機制。而且由RMSD與RMSF的圖表顯示出，經過修飾過後的核酸34與37位置，其值轉變為相當的大，代表說生物活性的增加趨勢。更進一步，我們發現三級結構鹼基配對(tertiary base pairs)與三鹼基配對(base triples)模擬後呈現階梯狀(stair-stepped)的構形。

We performed molecular dynamics (MD) simulation with the GROMOS96 force field to study the dynamical behavior of the wild-type human tRNA(Lys,3) with its 76 nucleotides (nt). The wild-type tRNA has mcm5s2U34 nucleotide at position 34 and ms2t6A37 nucleotide at position 37. The MD simulation time was 500 ps for studying conformational stability. Sodium counter ions were adopted to neutralize the tRNA system, and our results showed that tRNA(Lys,3) can be stabilized in sodium-ion solution. Analyzing the root mean square deviation (RMSD) of the tRNA, it is found that the L-shaped conformation of the 76-nt wild-type tRNA(Lys,3) was stable. The mechanisms for stability are rooted in formation of hydrogen bonds among base pairs. Hydrogen bonding among base triples is weak, and hence do not contribute stability. RMS deviations and RMS fluctuations of the modified nucleotides at positions 34 and 37 are larger, indicating increases of bonding strength and bioactivity. Furthermore, it is found that tertiary base pairs and base triples result in aligned conformation among nucleotides in three dimensions. We also observed canonical anticodon stair-stepped and stacking conformation in the tertiary structure.

[1] MacLeod, OT, McCarty M.,CM, Studies on the Chemical Nature of the Substance. Journal of Experimental Medicine, Vol. 79, 137-158. 1944.
[2] Crick F,Watson J, A Structure of Deoxyribonucleic Acid. Nature. Vol. 171, 737-738. 1953.
[3] Littlefield JW, Keller EB, Gross J, Zamecnik PC. Studies on Cytoplasmic Ribonucleoprotein Particles from the Liver of the Rat. Journal of Biological Chemistry, Vol. 217, 1955.
[4] EB, Zamecnik PC, Loftfield RB. The role of Microsomes in the Incorporation of Amino Acids into Proteins. Journal of Histochemistry and Cytochemistry, Vol. 2, 378-386, 1954.
[5] Marshall R, Nirenberg M. RNA Codons Recognized by Transfer RNA from Amphibian Embryos and Adults. Developmental biology,.Vol. 19, 1-11, 1969.
[6] Caskey CT, Beaudet A, Nirenberg M. RNA Codons and Protein Synthesis. 15. Dissimilar Responses of Mammalian and Bacterial Transfer RNA Fractions to Messenger RNA Codons. Journal of molecular biology, Vol. 37, 99-118, 1968.
[7] Caskey CT, Tompkins R, Scolnick E, Caryk T, Nirenberg M. Sequential Translation of Trinucleotide Codons for the Initiation and Termination of Protein Synthesis. Science, Vol. 162, 135-138, 1968.
[8] Scolnick E, Tompkins R, Caskey T, Nirenberg M. Release Factors Differing in Specificity for Terminator Codons. Proceedings of the National Academy of Sciences,Vol. 61,768-774. 1968.
[9] JG., Nirenberg M. Ribonucleic Acid Codons and Protein Synthesis. 13. RNA Codon Recognition by Deacylated tRNA and Aminoacyl-tRNA. Journal of molecular biology, Vol. 34, 467-480, 1968.
[10] Monod J, On the Mechanism of Molecular Interactions in the Control of Cellular Metabolism. Endocrinology.Vol. 78, 412-25, 1966.
[11] C, Cohn M, Kepes A, Monod J. Role of Lactose and Its Metabolic Products in the Induction of the Lactose Operon in Escherichia Coli. Biochimica et biophysica acta, Vol. 95, 634-639, 1965.
[12] Jacob F, Ullman A, Monod J. The Promotor, A Genetic Element Necessary to the Expression of an Operon. C R Hebd Seances Acad Sci. Vol. 258, 3125-3128, 1964.
[13] Jacob F, Monod J. Biochemical and Genetic Mechanisms of Regulation in the Bacterial Cell. Bulletin de la Société de chimie biologique. Vol. 46, 1499-1532, 1964.
[14] Berget SM, Berk AJ, Harrison T, Sharp PA. Spliced Segments at the
5' termini of Adenovirus-2 late mRNA: a Role for Heterogeneous
Nuclear RNA in Mammalian Cells. Cold Spring Harbor symposia on
quantitative biology, 42 Pt Vol. 1,523-529, 1978.
[15] Berget SM, Moore C, Sharp PA. Spliced Segments at the 5' terminus of Adenovirus 2 late mRNA. Proceedings of the National Academy of Sciences Vol. 74, 3171-3175. 1977.
[16] Berget SM, Sharp PA. A Spliced Sequence at the 5'-terminus of Adenovirus Late mRNA. Brookhaven symposia in biology, Vol.29, 332-344, 1977.
[17] Geerdes HA, Hilbers CW. The Iminoproton NMR Spectrum of Yeast tRNA-Phe Predicted from Crystal Coordinates. Nucleic Acids Research. Vol. 4, 207-221. 1977.
[18] Sussman JL, Holbrook SR, Warrant RW, Church GM, Kim SH. Crystal Structure of Yeast Phenylalanine Transfer RNA I. Crystallographic Refinement. Journal of molecular biology, Vol. 123, 607-630, 1978.
[19] Holbrook SR, Sussman JL, Warrant RW, Kim SH. Crystal Structure of Yeast Phenylalanine Transfer RNA *1: II. Structural Features and Functional Implications. J. Mol. Biol. 123:631-660. 1978.
[20] Comarmond MB, Giegé R, Thierry JC, Moras D, Fischer J. Three-dimensional Structure of Yeast tRNAAsp. I. Structure Determination. Acta Crystallographica Section B, Vol. 42, 272-280. 1986.
[21] Senger B, Aphasizhev R, Walter P, Fasiolo F. The Presence of a D-Stem but not a T-Stem is Essential for Triggering Aminoacylation upon Anticodon Binding in Yeast Methionine tRNA. Journal of molecular biology, Vol. 249, 45-58, 1995.
[22] Kelly NJ, Morrowb CD. Yeast tRNAPhe Expressed in Human Cells Can be Selected by HIV-1 for Use As A Reverse Transcription Primer. Virology Vol. 313, 354-363, 2003.
[23] Levinger L, Morl Mario and Florentz C. Survey and Summary Mitochondrial tRNA 3’End Metabolism and Human Disease. Nucleic Acids Research. Vol. 32, 5430-5441, 2004.
[24] Tomari Y, Hino N, Nagaike T, Suzuki T, Ueda T. Decreased CCA-addition in Human Mitochondrial tRNAs Bearing A Pathogenic A4317G or A10044 Mutation. Journal of Biological Chemistry, Vol. 278, 16828-16833, 2003.
[25] Hino N, Suzuki T, Yasukawa T, Seio K, Watanabe K, Ueda T. The Pathogenic A4269G Mutation in Human Mitochondrial tRNAIle Alters the T-stem Structure and Decreases the Binding Affinity for Elongation Factor Tu. Genes Cells, Vol. 9, 243-252, 2004.
[26] Wittenhagen LM, Kelley SO. Dimerization of A Pathogenic Human Mitochondrial tRNA. Nature Structural Biology, Vol. 9, 586-590, 2002.
[27] Sissler M, Helm M, Frugier M, Gieg_R, Florentz C. Aminoacylation Properties of Pathology-related variants of Human Mitochondrial tRNALys Variants. RNA. Vol. 10, 841-853, 2004.
[28] Renxiao Wang, Ying Fu, and Luhua Lai. A New Atom-Additive Method for Calculating Partition Coefficients. Journal of Chemical Information and Computer Sciences, Vol. 37, 615-621, 1997.
[29] Wang, R.; Gao, Y.; Liu, L.; Lai, L. All-Orientation Search and All-Placement Search in Comparative Molecular Field Analysis. Journal of Molecular Modeling, Vol. 4, 276-283, 1998.
[30] Wang, R.; Liu, L.; Lai, L.; Tang, Y. A New Empirical Method for Structure-Based Estimation of Binding Affinities. Journal of Molecular Modeling, Vol. 4, 379-394, 1998.
[31] Peng Tao, Renxiao Wang, and Luhua Lai. Calculating Partition Coefficients of Peptides by the Addition Method. Journal of Molecular Modeling, Vol. 5, 189-195, 1999.
[32] McCammon, J. A., and S. C. Harvey. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, New York, 1987.
[33] Ravishanker, G., P. Auffinger, D. R. Langley, B. Jayaram, M. A. Young, and D. L. Beveridge. Treatment of counterions in computer simulations of DNA. In Reviews in Computational Chemistry. K. B. Lipkowitz and D. B. Boyd, editors. VCH Publishers, New York. 317–372, 1997.
[34] Tapia, O., and I. Velazquez. Molecular dynamics simulation of DNA with protein’s consistent GROMOS force field and the role of counterions’ symmetry. Journal of the American Chemical Society, Vol. 119, 5934 –5938, 1997.
[35] Essmann, U., L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. A smooth particle mesh Ewald method. The Journal of Chemical Physics Vol. 103, 8577– 8593, 1995.
[36] P. Auffinger, S. Louise-May, and E. Westhof. Molecular dynamics simulations of solvated yeast tRNAASp. Biophysical Journal, Vol. 76, 50–64, 1999.
[37] Lindahl, E., Hess, B., van der Spoel, D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. Journal of Molecular Modeling, Vol. 7, 306-317, 2001.
[38] Scott, W. R. P., Hunenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Kruger, P., van Gunsteren, W. F. The GROMOS biomolecular simulation program package. The Journal of Chemical Physics A, Vol. 103, 3596-3607, 1999.

[39] Jorgensen,W. L., Chandrasekhar, J. and Madura, J. D. Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, Vol. 79, 926–935, 1983.
[40] Abseher, R., and Nilges, M. Are there non-trivial dynamic crosscorrelations in proteins? Journal of molecular biology, Vol. 279, 911–920, 1998.
[41] McCrate, N. E., Varner, M. E., Kim, K. I., Nagan, M. C. Molecular dynamics simulations of human tRNA (Lys,3)(UUU) : the role of modified bases in mRNA recognition. Nucleic acids research, Vol. 34, 5361-5368, 2006.
[42] Weerasinghe, S., Smith, P. E., and Pettitt, M. Structure and stability of a model pyrimidine-purine-purine DNA triple helix with a GCzT mismatch by simulation. Biochemistry, Vol. 34, 16269–16278, 1995.
[43] Genest, D. Motion of groups of atoms in DNA studied by molecular dynamics simulation. European Biophysics Journal, Vol. 27, 283–289, 1998
[44] Quigley, G. J., Rich, A. Structural domains of transfer RNA molecules. Science, Vol. 194, 796–806., 1976
[45] Saenger, W. Principles of Nucleic Acid Structure. Springer Verlag, New York, 1984.
[46] Kim, S. H., Quigley, G. J., Suddath, F. L., McPherson, A., Sneden, D., Kim, J. J., Weinzierl, J., Rich, A. Three-dimensional structure of yeast phenylalanine transfer RNA: Folding of the polynucleotide chain. Science, Vol. 179, 285–288, 1973
[47] Robertus, J. D., Ladner, J. E., Finch, J. T., Rhodes, D., Brown, R. S., Clark, B. F. Klug, A. Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature, Vol. 250, 546–551, 1974.
[48] Westhof, E., Dumas, P., Moras, D. Crystallographic refinement of yeast aspartic acid transfer RNA. Journal of molecular biology, Vol. 184, 119–145, 1985