201
6 Quantum Chemical Approaches in Modeling the Structure of DNA …
25. Murat P, Singh Y, Defrancq E (2011) Methods for investigating G-quadruplex DNA/ligand
interactions. Chem Soc Rev 40:5293–307
26. Palchaudhuri R, Hergenrother PJ (2007) DNA as a target for anticancer compounds: methods to determine the mode of binding and the mechanism of action. Curr Opin Biotechnol
18:497–503
27. Sun D, Hurley H (2010) Biochemical techniques for the characterization of G-quadruplex
structures: EMSA, DMS footprinting and DNA polymerase stop assay. Methods Mol Biol
608:65–79
28. Mergny J-L, Lacroix L (2009) UV melting of G-quadruplexes. Curr Protoc Nucleic Acid
Chem 37:17.1.1–17.1.15. doi: 10.1002/0471142700.nc1701s37
29. Olsen CM, Marky LA (2010) Monitoring the temperature unfolding of G-quadruplexes by
UV and circular dichroism spectroscopies and calorimetry techniques. Methods Mol Biol
608:147–158
30. Vorlíčková M, Kejnovská I, Sagi J, Renčiuk D, Bednářová K, Motlová J, Kypr J (2012) Circular dichroism and guanine quadruplexes. Methods 57:64–75
31. Juskowiak B, Takenaka S (2006) Fluorescence resonance energy transfer in the studies of
guanine quadruplexes. Methods Mol Biol. 335:311–341
32. Okumus B, Ha T (2010) Real-time observation of G-quadruplex dynamics using singlemolecule FRET microscopy. Methods Mol Biol 608: 81–96
33. De Cian A, Guittat L, Kaiser M, Saccà B, Amrane S, Bourdoncle A, Alberti P, TeuladeFichou M-P, Lacroix L, Mergny J-L (2007) Fluorescence-based melting assays for studying
quadruplex ligands. Methods 42:183–195
34. Zhao Y, Kan Z-y, Zeng Z-x, Hao Y-h, Chen H, Tan Z (2004) Determining the folding and
unfolding rate constants of nucleic acids by biosensor. application to telomere G-quadruplex.
J Am Chem Soc 126:13255–13264
35. Redman JE (2007) Surface plasmon resonance for probing quadruplex folding and interactions with proteins and small molecules. Methods 43:302–312
36. Schlachter C, Lisdat F, Frohme M, Erdmann VA, Konthur Z, Lehrach H, Glökler J (2012)
Pushing the detection limits: The evanescent field in surface plasmon resonance and analyteinduced folding observation of long human telomeric repeats. Biosens Bioelectron 31:571–
574
37. Parkinson GN, Lee MP, Neidle S (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417:876–880
38. Li J, Correia JJ, Wang L, Trent JO, Chaires JB (2005) Not so crystal clear: the structure of the
human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids
Res 33:4649–4659
39. Campbell NH, Parkinson GN (2007) Crystallographic studies of quadruplex nucleic acids.
Methods 43:252–263
40. Neidle S, Parkinson GN (2008) Quadruplex DNA crystal structures and drug design. Biochimie 90:1184–1196
41. Campbell N, Collie GW, Neidle S (2012) Crystallography of DNA and RNA G-quadruplex
nucleic acids and their ligand complexes. Curr Protoc Nucleic Acid Chem 50:17.6.1–17.6.22.
doi: 10.1002/0471142700.nc1706s50
42. Webba da Silva M (2007) NMR methods for studying quadruplex nucleic acids. Methods
43:264–277
43. Adrian M, Heddi B, Phan AT (2012) NMR spectroscopy of G-quadruplexes. Methods 57:11–24
44. Hehre JW, Radom L, Schleyer P, Pople J (1986) Ab initio molecular orbital theory. John Wiley
and Sons, New York
45. Berkert U, Allinger NL (1982) Molecular Mechanics. American Chem Soc Washington, DC
46. Tsai SC (2007) Biomacromolecules. Introduction to Structure, Function and Informatics.
Wiley-Liss, New York p. 249–288
47. Šponer J, Šponer JE, Mládek A, Jurečka P, Banáš P, Otyepka M (2013) Nature and magnitude
of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and
experiment. Biopolym, 99, 978–988.
6 Quantum Chemical Approaches in Modeling the Structure of DNA …
25. Murat P, Singh Y, Defrancq E (2011) Methods for investigating G-quadruplex DNA/ligand
interactions. Chem Soc Rev 40:5293–307
26. Palchaudhuri R, Hergenrother PJ (2007) DNA as a target for anticancer compounds: methods to determine the mode of binding and the mechanism of action. Curr Opin Biotechnol
18:497–503
27. Sun D, Hurley H (2010) Biochemical techniques for the characterization of G-quadruplex
structures: EMSA, DMS footprinting and DNA polymerase stop assay. Methods Mol Biol
608:65–79
28. Mergny J-L, Lacroix L (2009) UV melting of G-quadruplexes. Curr Protoc Nucleic Acid
Chem 37:17.1.1–17.1.15. doi: 10.1002/0471142700.nc1701s37
29. Olsen CM, Marky LA (2010) Monitoring the temperature unfolding of G-quadruplexes by
UV and circular dichroism spectroscopies and calorimetry techniques. Methods Mol Biol
608:147–158
30. Vorlíčková M, Kejnovská I, Sagi J, Renčiuk D, Bednářová K, Motlová J, Kypr J (2012) Circular dichroism and guanine quadruplexes. Methods 57:64–75
31. Juskowiak B, Takenaka S (2006) Fluorescence resonance energy transfer in the studies of
guanine quadruplexes. Methods Mol Biol. 335:311–341
32. Okumus B, Ha T (2010) Real-time observation of G-quadruplex dynamics using singlemolecule FRET microscopy. Methods Mol Biol 608: 81–96
33. De Cian A, Guittat L, Kaiser M, Saccà B, Amrane S, Bourdoncle A, Alberti P, TeuladeFichou M-P, Lacroix L, Mergny J-L (2007) Fluorescence-based melting assays for studying
quadruplex ligands. Methods 42:183–195
34. Zhao Y, Kan Z-y, Zeng Z-x, Hao Y-h, Chen H, Tan Z (2004) Determining the folding and
unfolding rate constants of nucleic acids by biosensor. application to telomere G-quadruplex.
J Am Chem Soc 126:13255–13264
35. Redman JE (2007) Surface plasmon resonance for probing quadruplex folding and interactions with proteins and small molecules. Methods 43:302–312
36. Schlachter C, Lisdat F, Frohme M, Erdmann VA, Konthur Z, Lehrach H, Glökler J (2012)
Pushing the detection limits: The evanescent field in surface plasmon resonance and analyteinduced folding observation of long human telomeric repeats. Biosens Bioelectron 31:571–
574
37. Parkinson GN, Lee MP, Neidle S (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417:876–880
38. Li J, Correia JJ, Wang L, Trent JO, Chaires JB (2005) Not so crystal clear: the structure of the
human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids
Res 33:4649–4659
39. Campbell NH, Parkinson GN (2007) Crystallographic studies of quadruplex nucleic acids.
Methods 43:252–263
40. Neidle S, Parkinson GN (2008) Quadruplex DNA crystal structures and drug design. Biochimie 90:1184–1196
41. Campbell N, Collie GW, Neidle S (2012) Crystallography of DNA and RNA G-quadruplex
nucleic acids and their ligand complexes. Curr Protoc Nucleic Acid Chem 50:17.6.1–17.6.22.
doi: 10.1002/0471142700.nc1706s50
42. Webba da Silva M (2007) NMR methods for studying quadruplex nucleic acids. Methods
43:264–277
43. Adrian M, Heddi B, Phan AT (2012) NMR spectroscopy of G-quadruplexes. Methods 57:11–24
44. Hehre JW, Radom L, Schleyer P, Pople J (1986) Ab initio molecular orbital theory. John Wiley
and Sons, New York
45. Berkert U, Allinger NL (1982) Molecular Mechanics. American Chem Soc Washington, DC
46. Tsai SC (2007) Biomacromolecules. Introduction to Structure, Function and Informatics.
Wiley-Liss, New York p. 249–288
47. Šponer J, Šponer JE, Mládek A, Jurečka P, Banáš P, Otyepka M (2013) Nature and magnitude
of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and
experiment. Biopolym, 99, 978–988.