75. Biesiada M, Purzycka KJ, Szachniuk M, Blazewicz J, Adamiak RW (2016) Automated RNA
3D structure prediction with RNA composer. Methods Mol Biol 1490:199–215
76. Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C,
Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferr-D’Amar AR, Das R, Ding F, Dokholyan
NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann
TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A,
Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T,
Westhof E (2015) RNA-puzzles round II: assessment of RNA structure prediction programs
applied to three large RNA structures. RNA 21:1–19
77. Thirumalai D (1998) Native secondary structure formation in RNA may be a slave to tertiary
folding. Proc Natl Acad Sci U S A 95:11506–11508
78. van Holde KE, Johnson WC, Ho PS (1998) Principles of physical biochemistry. Prentice Hall,
Upper Saddle River, pp 9–11
79. Karshikoff A (2006) Non covalent interactions in proteins. Imperial College Press, London.
ISBN: 978-1-86094-707-0
80. Blanco C, Bayas M, Yan F, Chen IA (2018) Analysis of evolutionarily independent proteinRNA complexes yields a criterion to evaluate the relevance of prebiotic scenarios. Curr Biol
28:526–537
81. Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS (2010) Origins of specificity in proteinDNA recognition. Annu Rev Biochem 79:233–269
82. Privalov PL, Dragan AI, Crane-Robinson C (2011) Interpreting protein/DNA interactions:
distinguishing specific from non-specific and electrostatic from non-electrostatic components.
Nucleic Acids Res 7:2483–2491
83. Wells RA, Kellie JL, Wetmore SD (2013) Significant strength of charged DNA-protein π-π
interactions: a preliminary study of cytosine. J Phys Chem B 117:10462–10474
84. Kim H, Jeong E, Lee SW, Han K (2003) Computational analysis of hydrogen bonds in proteinRNA complexes for interaction patterns. FEBS Lett 552:231–239
85. Nobeli I, Laskowski RA, Valdar WSJ, Thornton JM (2001) On the molecular discrimination
between adenine and guanine by proteins. Nucleic Acids Res 29:4294–4309
86. Baldauf C, Gunther R, Hofmann HJ (2006) Theoretical prediction of the basic helix types in α,
β-hybrid peptides. Biopolymers 84:408–413
87. Tolstorukov MY, Jernigan RL, Zhurkin VB (2004) Protein–DNA hydrophobic recognition in
the minor groove is facilitated by sugar switching. J Mol Biol 337:65–76
88. Su Y, Yamashita MM, Greasley SE, Mullen CA, Shim JH, Jennings PA, Benkovic SJ, Wilson
IA (1998) A pH-dependent stabilization of an active site loop observed from low and high pH
crystal structures of mutant monomeric glycinamide ribonucleotide transformylase at 1.8 to
1.9 A. J Biol Mol 281:485–499
89. Gilson MK, Given GA, Bush BL, McCammon JA (1997) The statistical-thermodynamic basis
for computation of binding affinities. Biophys J 72:1047–1069
90. Nguyen QN, Perret G, Ducongé F (2016) Applications of high-throughput sequencing for
in vitro selection and characterization of aptamers. Pharmaceuticals (Basel) 9:E76
91. Beck TF, Mullikin JC, Biesecker LG (2016) Systematic evaluation of Sanger validation of
next-generation sequencing variants. Clin Chem 62:647–654
92. Ouyang W, Yu Z, Zhao X, Lu S, Wang Z (2016) Aptamers in hematological malignancies and
their potential therapeutic implications. Crit Rev Oncol Hematol 106:108–117
93. Morita Y, Leslie M, Kameyama H, Volk DE, Tanaka T (2018) Aptamer therapeutics in cancer:
current and future. Cancer 10:e80
94. Zhu Q, Liu G, Kai M (2015) DNA aptamers in the diagnosis and treatment of human diseases.
Molecules 20:20979–20997
95. Molefe PF, Masamba P, Oyinloye BE, Mbatha LS, Meyer M, Kappo AP (2019) Molecular
application of aptamers in the diagnosis and treatment of cancer and communicable diseases.
Pharmaceuticals 11:e93
96. Zhou J, Rossi J (2017) Aptamers as targeted therapeutics: current potential and challenges. Nat
Rev Drug Discov 16:181–202
134
G. Perret and E. Boschetti
3D structure prediction with RNA composer. Methods Mol Biol 1490:199–215
76. Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C,
Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferr-D’Amar AR, Das R, Ding F, Dokholyan
NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann
TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A,
Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T,
Westhof E (2015) RNA-puzzles round II: assessment of RNA structure prediction programs
applied to three large RNA structures. RNA 21:1–19
77. Thirumalai D (1998) Native secondary structure formation in RNA may be a slave to tertiary
folding. Proc Natl Acad Sci U S A 95:11506–11508
78. van Holde KE, Johnson WC, Ho PS (1998) Principles of physical biochemistry. Prentice Hall,
Upper Saddle River, pp 9–11
79. Karshikoff A (2006) Non covalent interactions in proteins. Imperial College Press, London.
ISBN: 978-1-86094-707-0
80. Blanco C, Bayas M, Yan F, Chen IA (2018) Analysis of evolutionarily independent proteinRNA complexes yields a criterion to evaluate the relevance of prebiotic scenarios. Curr Biol
28:526–537
81. Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS (2010) Origins of specificity in proteinDNA recognition. Annu Rev Biochem 79:233–269
82. Privalov PL, Dragan AI, Crane-Robinson C (2011) Interpreting protein/DNA interactions:
distinguishing specific from non-specific and electrostatic from non-electrostatic components.
Nucleic Acids Res 7:2483–2491
83. Wells RA, Kellie JL, Wetmore SD (2013) Significant strength of charged DNA-protein π-π
interactions: a preliminary study of cytosine. J Phys Chem B 117:10462–10474
84. Kim H, Jeong E, Lee SW, Han K (2003) Computational analysis of hydrogen bonds in proteinRNA complexes for interaction patterns. FEBS Lett 552:231–239
85. Nobeli I, Laskowski RA, Valdar WSJ, Thornton JM (2001) On the molecular discrimination
between adenine and guanine by proteins. Nucleic Acids Res 29:4294–4309
86. Baldauf C, Gunther R, Hofmann HJ (2006) Theoretical prediction of the basic helix types in α,
β-hybrid peptides. Biopolymers 84:408–413
87. Tolstorukov MY, Jernigan RL, Zhurkin VB (2004) Protein–DNA hydrophobic recognition in
the minor groove is facilitated by sugar switching. J Mol Biol 337:65–76
88. Su Y, Yamashita MM, Greasley SE, Mullen CA, Shim JH, Jennings PA, Benkovic SJ, Wilson
IA (1998) A pH-dependent stabilization of an active site loop observed from low and high pH
crystal structures of mutant monomeric glycinamide ribonucleotide transformylase at 1.8 to
1.9 A. J Biol Mol 281:485–499
89. Gilson MK, Given GA, Bush BL, McCammon JA (1997) The statistical-thermodynamic basis
for computation of binding affinities. Biophys J 72:1047–1069
90. Nguyen QN, Perret G, Ducongé F (2016) Applications of high-throughput sequencing for
in vitro selection and characterization of aptamers. Pharmaceuticals (Basel) 9:E76
91. Beck TF, Mullikin JC, Biesecker LG (2016) Systematic evaluation of Sanger validation of
next-generation sequencing variants. Clin Chem 62:647–654
92. Ouyang W, Yu Z, Zhao X, Lu S, Wang Z (2016) Aptamers in hematological malignancies and
their potential therapeutic implications. Crit Rev Oncol Hematol 106:108–117
93. Morita Y, Leslie M, Kameyama H, Volk DE, Tanaka T (2018) Aptamer therapeutics in cancer:
current and future. Cancer 10:e80
94. Zhu Q, Liu G, Kai M (2015) DNA aptamers in the diagnosis and treatment of human diseases.
Molecules 20:20979–20997
95. Molefe PF, Masamba P, Oyinloye BE, Mbatha LS, Meyer M, Kappo AP (2019) Molecular
application of aptamers in the diagnosis and treatment of cancer and communicable diseases.
Pharmaceuticals 11:e93
96. Zhou J, Rossi J (2017) Aptamers as targeted therapeutics: current potential and challenges. Nat
Rev Drug Discov 16:181–202
134
G. Perret and E. Boschetti