Coarse-Grained Modeling and Simulations of Thermoresponsive …
69
29. Askari FK, McDonnell WM (1996) Antisense-oligonucleotide therapy. N Engl J Med
334(5):316–318
30. Uhlmann E, Peyman A (1990) Antisense oligonucleotides: a new therapeutic principle. Chem
Rev 90(4):543–584
31. Lee L, Johnston AP, Caruso F (2008) Manipulating the salt and thermal stability of DNA
multilayer films via oligonucleotide length. Biomacromol 9(11):3070–3078
32. Nakano S-I, Sugimoto N (2016) The structural stability and catalytic activity of DNA and
RNA oligonucleotides in the presence of organic solvents. Biophys Rev 8(1):11–23
33. Gibbs JM, Park S-J, Anderson DR, Watson KJ, Mirkin CA, Nguyen ST (2005) Polymer− DNA
hybrids as electrochemical probes for the detection of DNA. J Am Chem Soc 127(4):1170–
1178
34. Nielsen PE, Egholm M, Berg RH, Buchardt O (1991) Sequence-selective recognition of DNA
by strand displacement with a thymine-substituted polyamide. Science 254(5037):1497–1500
35. El-Sagheer AH, Brown T (2012) Click nucleic acid ligation: applications in biology and
nanotechnology. Acc Chem Res 45(8):1258–1267
36. Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, Meldgaard M, Olsen CE,
Wengel J (1998) LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine,
5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and
unprecedented nucleic acid recognition. Tetrahedron 54(14):3607–3630
37. Eschenmoser A (1999) Chemical etiology of nucleic acid structure. Science 284(5423):2118–
2124
38. Vilaivan T (2015) Pyrrolidinyl PNA with α/β-dipeptide backbone: from development to
applications. Acc Chem Res 48(6):1645–1656
39. Ichida JK, Horhota A, Zou K, McLaughlin LW, Szostak JW (2005) High fidelity TNA
synthesis by therminator polymerase. Nucleic Acids Res 33(16):5219–5225
40. Breslauer KJ, Frank R, Blöcker H, Marky LA (1986) Predicting DNA duplex stability from
the base sequence. Proc Natl Acad Sci 83(11):3746–3750
41. Sugimoto N, Nakano S-I, Yoneyama M, Honda K-I (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res
24(22):4501–4505
42. SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearestneighbor thermodynamics. Proc Natl Acad Sci 95(4):1460–1465
43. Zuker MJ (2003) Mfold web server for nucleic acid folding and hybridization prediction.
Nucleic Acid Res 31(13):3406–3415
44. Sugimoto N, Satoh N, Yasuda K, Nakano S-I (2001) Stabilization factors affecting duplex
formation of peptide nucleic acid with DNA. Biochemistry 40(29):8444–8451
45. Owczarzy R, You Y, Groth CL, Tataurov AV (2011) Stability and mismatch discrimination
of locked nucleic acid–DNA duplexes. Biochemistry 50(43):9352–9367
46. Dilek I, Madrid M, Singh R, Urrea CP, Armitage BA (2005) Effect of PNA backbone modifications on cyanine dye binding to PNA− DNA duplexes investigated by optical spectroscopy
and molecular dynamics simulations. J Am Chem Soc 127(10):3339–3345
47. Ortega J-A, Blas JR, Orozco M, Grandas A, Pedroso E, Robles J (2007) Binding affinities
of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are
unusually sequence-dependent. Org Lett 9(22):4503–4506
48. Siriwong K, Chuichay P, Saen-oon S, Suparpprom C, Vilaivan T, Hannongbua S (2008) Insight
into why pyrrolidinyl peptide nucleic acid binding to DNA is more stable than the DNA DNA
duplex. Biochem Biophys Res Commun 372(4):765–771
49. Sharma S, Sonavane UB, Joshi RR (2010) Molecular dynamics simulations of cyclohexyl
modified peptide nucleic acids (PNA). J Biomol Struct Dyn 27(5):663–676
50. Wierzbinski E, de Leon A, Yin X, Balaeff A, Davis KL, Reppireddy S, Venkatramani R,
Keinan S, Ly DH, Madrid M (2012) Effect of backbone flexibility on charge transfer rates in
peptide nucleic acid duplexes. J Am Chem Soc 134(22):9335–9342
51. Poomsuk N, Siriwong K (2013) Structural properties and stability of PNA with (2 R, 4
R)-and (2 R, 4 S)-prolyl-(1S, 2S)-2-aminocyclopentanecarboxylic acid backbone binding to
DNA: a molecular dynamics simulation study. Chem Phys Lett 588:237–241
69
29. Askari FK, McDonnell WM (1996) Antisense-oligonucleotide therapy. N Engl J Med
334(5):316–318
30. Uhlmann E, Peyman A (1990) Antisense oligonucleotides: a new therapeutic principle. Chem
Rev 90(4):543–584
31. Lee L, Johnston AP, Caruso F (2008) Manipulating the salt and thermal stability of DNA
multilayer films via oligonucleotide length. Biomacromol 9(11):3070–3078
32. Nakano S-I, Sugimoto N (2016) The structural stability and catalytic activity of DNA and
RNA oligonucleotides in the presence of organic solvents. Biophys Rev 8(1):11–23
33. Gibbs JM, Park S-J, Anderson DR, Watson KJ, Mirkin CA, Nguyen ST (2005) Polymer− DNA
hybrids as electrochemical probes for the detection of DNA. J Am Chem Soc 127(4):1170–
1178
34. Nielsen PE, Egholm M, Berg RH, Buchardt O (1991) Sequence-selective recognition of DNA
by strand displacement with a thymine-substituted polyamide. Science 254(5037):1497–1500
35. El-Sagheer AH, Brown T (2012) Click nucleic acid ligation: applications in biology and
nanotechnology. Acc Chem Res 45(8):1258–1267
36. Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, Meldgaard M, Olsen CE,
Wengel J (1998) LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine,
5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and
unprecedented nucleic acid recognition. Tetrahedron 54(14):3607–3630
37. Eschenmoser A (1999) Chemical etiology of nucleic acid structure. Science 284(5423):2118–
2124
38. Vilaivan T (2015) Pyrrolidinyl PNA with α/β-dipeptide backbone: from development to
applications. Acc Chem Res 48(6):1645–1656
39. Ichida JK, Horhota A, Zou K, McLaughlin LW, Szostak JW (2005) High fidelity TNA
synthesis by therminator polymerase. Nucleic Acids Res 33(16):5219–5225
40. Breslauer KJ, Frank R, Blöcker H, Marky LA (1986) Predicting DNA duplex stability from
the base sequence. Proc Natl Acad Sci 83(11):3746–3750
41. Sugimoto N, Nakano S-I, Yoneyama M, Honda K-I (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res
24(22):4501–4505
42. SantaLucia J (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearestneighbor thermodynamics. Proc Natl Acad Sci 95(4):1460–1465
43. Zuker MJ (2003) Mfold web server for nucleic acid folding and hybridization prediction.
Nucleic Acid Res 31(13):3406–3415
44. Sugimoto N, Satoh N, Yasuda K, Nakano S-I (2001) Stabilization factors affecting duplex
formation of peptide nucleic acid with DNA. Biochemistry 40(29):8444–8451
45. Owczarzy R, You Y, Groth CL, Tataurov AV (2011) Stability and mismatch discrimination
of locked nucleic acid–DNA duplexes. Biochemistry 50(43):9352–9367
46. Dilek I, Madrid M, Singh R, Urrea CP, Armitage BA (2005) Effect of PNA backbone modifications on cyanine dye binding to PNA− DNA duplexes investigated by optical spectroscopy
and molecular dynamics simulations. J Am Chem Soc 127(10):3339–3345
47. Ortega J-A, Blas JR, Orozco M, Grandas A, Pedroso E, Robles J (2007) Binding affinities
of oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogues are
unusually sequence-dependent. Org Lett 9(22):4503–4506
48. Siriwong K, Chuichay P, Saen-oon S, Suparpprom C, Vilaivan T, Hannongbua S (2008) Insight
into why pyrrolidinyl peptide nucleic acid binding to DNA is more stable than the DNA DNA
duplex. Biochem Biophys Res Commun 372(4):765–771
49. Sharma S, Sonavane UB, Joshi RR (2010) Molecular dynamics simulations of cyclohexyl
modified peptide nucleic acids (PNA). J Biomol Struct Dyn 27(5):663–676
50. Wierzbinski E, de Leon A, Yin X, Balaeff A, Davis KL, Reppireddy S, Venkatramani R,
Keinan S, Ly DH, Madrid M (2012) Effect of backbone flexibility on charge transfer rates in
peptide nucleic acid duplexes. J Am Chem Soc 134(22):9335–9342
51. Poomsuk N, Siriwong K (2013) Structural properties and stability of PNA with (2 R, 4
R)-and (2 R, 4 S)-prolyl-(1S, 2S)-2-aminocyclopentanecarboxylic acid backbone binding to
DNA: a molecular dynamics simulation study. Chem Phys Lett 588:237–241