70
A. Jayaraman et al.
52. Gupta SK, Sur S, Ojha RP, Tandon V (2013) Influence of PNA containing 8-aza-7deazaadenine on structure stability and binding affinity of PNA·DNA duplex: insights from
thermodynamics, counter ion, hydration and molecular dynamics analysis. Mol BioSyst
9(7):1958–1971
53. Autiero I, Saviano M, Langella E (2014) Molecular dynamics simulations of PNA–PNA and
PNA–DNA duplexes by the use of new parameters implemented in the GROMACS package:
a conformational and dynamics study. Phys Chem Chem Phys 16(5):1868–1874
54. Autiero I, Saviano M, Langella E (2015) Conformational studies of chiral D-Lys-PNA and
achiral PNA system in binding with DNA or RNA through a molecular dynamics approach.
Eur J Med Chem 91:109–117
55. Petersen M, Håkansson AE, Wengel J, Jacobsen JP (2001) α-l-LNA (α-i-r ibo configured
locked nucleic acid) recognition of RNA. A study by NMR spectroscopy and molecular
dynamics simulations. J Am Chem Soc 123(30):7431–7432
56. Ivanova A, Rösch N (2007) The structure of LNA: DNA hybrids from molecular dynamics
simulations: the effect of locked nucleotides. J Phys Chem A 111(38):9307–9319
57. Pande V, Nilsson L (2008) Insights into structure, dynamics and hydration of locked nucleic
acid (LNA) strand-based duplexes from molecular dynamics simulations. Nucleic Acids Res
36(5):1508–1516
58. Hudson GA, Bloomingdale RJ, Znosko BM (2013) Thermodynamic contribution and nearestneighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides. RNA
19(11):1474–1482
59. Theodorakis PE, Fytas NG, Kahl G, Dellago C (2015) Self-assembly of DNA-functionalized
colloids. arXiv:1503.05384
60. Dai W, Hsu CW, Sciortino F, Starr FW (2009) Valency dependence of polymorphism and
polyamorphism in dna-functionalized nanoparticles. Langmuir 26(5):3601–3608
61. Knorowski C, Burleigh S, Travesset A (2011) Dynamics and statics of DNA-programmable
nanoparticle self-assembly and crystallization. Phys Rev Lett 106(21):215501
62. Li TI, Sknepnek R, Macfarlane RJ, Mirkin CA, Olvera de la Cruz M (2012) Modeling the
crystallization of spherical nucleic acid nanoparticle conjugates with molecular dynamics
simulations. Nano Lett 12(5):2509–2514
63. Kenward M, Dorfman KD (2009) Brownian dynamics simulations of single-stranded DNA
hairpins. J Chem Phys 130(9):03B602
64. Kenward M, Dorfman KD (2009) Coarse-grained brownian dynamics simulations of the
10–23 DNAzyme. Biophys J 97(10):2785–2793
65. Ding Y, Mittal J (2014) Insights into DNA-mediated interparticle interactions from a coarsegrained model. J Chem Phys 141(18):11B608_1
66. Condon JE, Jayaraman A (2017) Effect of oligonucleic acid (ONA) backbone features on
assembly of ONA–star polymer conjugates: a coarse-grained molecular simulation study.
Soft Matter 13(38):6770–6783
67. Prhashanna A, Jayaraman A (2019) Melting thermodynamics of oligonucleic acids conjugated
with relatively solvophobic linear polymers: a coarse-grained molecular simulation study. J
Polym Sci Part B Polym Phys 57(18):1196–208
68. Andersen HC (1983) Rattle: a “velocity” version of the shake algorithm for molecular
dynamics calculations. J Comput Phys 52(1):24–34
69. Jones JE (1924) On the determination of molecular fields.—II. From the equation of state of
a gas. Proc Roy Soc Lond Ser A Containing Papers Math Phys Charact 106 (738):463–477
70. Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E (2015) GROMACS:
High performance molecular simulations through multi-level parallelism from laptops to
supercomputers. SoftwareX 1:19–25
71. Weeks JD, Chandler D, Andersen HC (1971) Role of repulsive forces in determining the
equilibrium structure of simple liquids. J Chem Phys 54(12):5237–5247
72. Stogryn A (1971) Equations for calculating the dielectric constant of saline water (correspondence). IEEE Trans Microw Theory Tech 19(8):733–736
A. Jayaraman et al.
52. Gupta SK, Sur S, Ojha RP, Tandon V (2013) Influence of PNA containing 8-aza-7deazaadenine on structure stability and binding affinity of PNA·DNA duplex: insights from
thermodynamics, counter ion, hydration and molecular dynamics analysis. Mol BioSyst
9(7):1958–1971
53. Autiero I, Saviano M, Langella E (2014) Molecular dynamics simulations of PNA–PNA and
PNA–DNA duplexes by the use of new parameters implemented in the GROMACS package:
a conformational and dynamics study. Phys Chem Chem Phys 16(5):1868–1874
54. Autiero I, Saviano M, Langella E (2015) Conformational studies of chiral D-Lys-PNA and
achiral PNA system in binding with DNA or RNA through a molecular dynamics approach.
Eur J Med Chem 91:109–117
55. Petersen M, Håkansson AE, Wengel J, Jacobsen JP (2001) α-l-LNA (α-i-r ibo configured
locked nucleic acid) recognition of RNA. A study by NMR spectroscopy and molecular
dynamics simulations. J Am Chem Soc 123(30):7431–7432
56. Ivanova A, Rösch N (2007) The structure of LNA: DNA hybrids from molecular dynamics
simulations: the effect of locked nucleotides. J Phys Chem A 111(38):9307–9319
57. Pande V, Nilsson L (2008) Insights into structure, dynamics and hydration of locked nucleic
acid (LNA) strand-based duplexes from molecular dynamics simulations. Nucleic Acids Res
36(5):1508–1516
58. Hudson GA, Bloomingdale RJ, Znosko BM (2013) Thermodynamic contribution and nearestneighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides. RNA
19(11):1474–1482
59. Theodorakis PE, Fytas NG, Kahl G, Dellago C (2015) Self-assembly of DNA-functionalized
colloids. arXiv:1503.05384
60. Dai W, Hsu CW, Sciortino F, Starr FW (2009) Valency dependence of polymorphism and
polyamorphism in dna-functionalized nanoparticles. Langmuir 26(5):3601–3608
61. Knorowski C, Burleigh S, Travesset A (2011) Dynamics and statics of DNA-programmable
nanoparticle self-assembly and crystallization. Phys Rev Lett 106(21):215501
62. Li TI, Sknepnek R, Macfarlane RJ, Mirkin CA, Olvera de la Cruz M (2012) Modeling the
crystallization of spherical nucleic acid nanoparticle conjugates with molecular dynamics
simulations. Nano Lett 12(5):2509–2514
63. Kenward M, Dorfman KD (2009) Brownian dynamics simulations of single-stranded DNA
hairpins. J Chem Phys 130(9):03B602
64. Kenward M, Dorfman KD (2009) Coarse-grained brownian dynamics simulations of the
10–23 DNAzyme. Biophys J 97(10):2785–2793
65. Ding Y, Mittal J (2014) Insights into DNA-mediated interparticle interactions from a coarsegrained model. J Chem Phys 141(18):11B608_1
66. Condon JE, Jayaraman A (2017) Effect of oligonucleic acid (ONA) backbone features on
assembly of ONA–star polymer conjugates: a coarse-grained molecular simulation study.
Soft Matter 13(38):6770–6783
67. Prhashanna A, Jayaraman A (2019) Melting thermodynamics of oligonucleic acids conjugated
with relatively solvophobic linear polymers: a coarse-grained molecular simulation study. J
Polym Sci Part B Polym Phys 57(18):1196–208
68. Andersen HC (1983) Rattle: a “velocity” version of the shake algorithm for molecular
dynamics calculations. J Comput Phys 52(1):24–34
69. Jones JE (1924) On the determination of molecular fields.—II. From the equation of state of
a gas. Proc Roy Soc Lond Ser A Containing Papers Math Phys Charact 106 (738):463–477
70. Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E (2015) GROMACS:
High performance molecular simulations through multi-level parallelism from laptops to
supercomputers. SoftwareX 1:19–25
71. Weeks JD, Chandler D, Andersen HC (1971) Role of repulsive forces in determining the
equilibrium structure of simple liquids. J Chem Phys 54(12):5237–5247
72. Stogryn A (1971) Equations for calculating the dielectric constant of saline water (correspondence). IEEE Trans Microw Theory Tech 19(8):733–736