Skip to main content
Article thumbnail
Location of Repository

Circular dichroism and conformational polymorphism of DNA

By Jaroslav Kypr, Iva Kejnovská, Daniel Renčiuk and Michaela Vorlíčková


Here we review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy. The conformational properties include the B-family of structures, A-form, Z-form, guanine quadruplexes, cytosine quadruplexes, triplexes and other less characterized structures. CD spectroscopy is extremely sensitive and relatively inexpensive. This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules. The samples can easily be titrated with various agents to cause conformational isomerizations of DNA. The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states. It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters. In careful hands, CD spectroscopy is a valuable tool for mapping conformational properties of particular DNA molecules. Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA

Topics: Survey and Summary
Publisher: Oxford University Press
OAI identifier:
Provided by: PubMed Central

Suggested articles


  1. (2000). A nuclease hypersensitive element in the human c-myc promoter adopts several distinct i-tetraplex structures.
  2. (2001). A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC).
  3. (1995). Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes.
  4. (1987). Absorption, scattering, and imaging of biomolecular structures by polarized-light.
  5. (1992). Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex.
  6. (2000). An A-type double helix of DNA having B-type puckering of the deoxyribose rings.
  7. (2003). Analysis of thermal melting curves.
  8. (1999). Aqueous trifluorethanol solutions simulate the environment of DNA in the crystalline state.
  9. (2003). Biophysical and biological properties of quadruplex oligodeoxyribonucleotides.
  10. (2007). Biophysical characterization of the human telomeric (TTAGGG)4 repeat in a potassium solution.
  11. (1987). Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves.
  12. (1970). Circular dichroism of DNA films: reversibility studies.
  13. (1998). Circular dichroism of DNA frayed wires.
  14. (1974). Circular dichroism of DNA in the vacuum ultraviolet.
  15. (1972). Circular dichroism of DNA: temperature and salt dependence.
  16. (2007). Circular dichroism of quadruplex DNAs: applications to structure, cation effects and ligand binding.
  17. (1991). Circular Dichroism Principles and Applications.
  18. (1992). Circular dichroism spectroscopy of DNA.
  19. (2002). Circular dichroism spectroscopy reveals invariant conformation of guanine runs in DNA.
  20. (1995). Circular dichroism.
  21. (1996). Comparison of the solution and crystal conformations of (G+C)-rich fragments of DNA.
  22. (1988). Conformation of the synthetic DNA poly(amino 2dA-dT) duplex in high-salt and aqueous alcohol solutions.
  23. (2003). Conformational polymorphism of d(A-G)n and related oligonucleotide sequences.
  24. (1992). Conformational transitions of poly(dA-bromo 5dU) and poly(dA-iodo 5dU) in solution.
  25. (1982). Conformational transitions of poly(dA-dT) poly(dA-dT) in ethanolic solutions.
  26. (1985). Conformational variability of poly(dA-dT).poly(dA-dT) and some other deoxyribonucleic acids includes a novel type of double helix.
  27. (2001). Conserved guanine-guanine stacking in tetraplex and duplex DNA.
  28. (1984). Cooperative changes in the chiroptical properties of DNA induced by methanol.
  29. (2002). Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing.
  30. (2002). Crystal structure of parallel quadruplexes from human telomeric DNA.
  31. (1996). Determination of the Conformation of Nucleic Acids by Electronic CD.
  32. (1973). Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism.
  33. (2006). Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K + solution.
  34. (2001). Dimethylsulfoxide-stabilized conformer of guanine-adenine repeat strand of DNA.
  35. (2008). Discovery of alternative DNA structures: a heroic decade (1979-1989).
  36. (1995). Divalent zinc cations induce the formation of two distinct homoduplexes of a d(GA)20 DNA sequence.
  37. (2004). DNA as a ‘nanomaterial’.
  38. (2008). DNA triple helices: biological consequences and therapeutic potential.
  39. (1981). Effects of methylation on a synthetic polynucleotide: the B-Z transition in poly(dGm 5dC).poly(dG-m 5dC).
  40. (2006). Ethanol is a better inducer of DNA guanine tetraplexes than potassium cations.
  41. (1994). Evidence for intramolecularly folded i-DNA structures in biologically relevant CCC-repeat sequences.
  42. (1986). Graphical analysis of circular dichroic spectra distinguishes between two-state and gradual alterations in DNA conformation.
  43. (2005). Guanine tetraplex topology of human telomere DNA is governed by the number of (TTAGGG) repeats.
  44. (1992). Hairpin and parallel quartet structures for telomeric sequences.
  45. (2005). Highly prevalent putative quadruplex sequence motifs in human DNA.
  46. (2006). Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution.
  47. (2007). Intramolecular and intermolecular guanine quadruplexes of DNA in aqueous salt and ethanol solutions.
  48. (1995). Intramolecular folding of pyrimidine oligodeoxynucleotides into a I-DNA motif.
  49. (2008). Ligands playing musical chairs with G-quadruplex DNA: a rapid and simple displacement assay for identifying selective G-quadruplex binders.
  50. (2008). Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities.
  51. (2008). Molecular dynamics and principal components analysis of human telomeric quadruplex multimers.
  52. (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution.
  53. (2007). Non-B DNA conformations, mutagenesis and disease.
  54. (2005). Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal.
  55. (1999). Nucleic Acid Structure.
  56. (2000). Parallel intramolecular DNA triple helix with G and T bases in the third strand stabilized by Zn 2+ ions.
  57. (1997). Parallel-stranded linear homoduplexes of d(A +-G)n>10 and d(A-G)n>10 manifesting the contrasting ionic strength sensitivities of poly(A
  58. (1970). Physical and enzymatic studies on poly d(I-C)-poly d(I-C), an unusual double-helical DNA.
  59. (1988). Poly(amino 2dA-dT) isomerizes into the unusual X-DNA double helix at physiological conditions inducing Z-DNA in poly (dG-methyl 5dC).
  60. (1985). Poly(d2NH2A-dT): two-dimensional NMR shows a B to A conversion in high salt.
  61. (2008). Polymorphism of human telomeric quadruplex structures.
  62. (2007). Possibility of an antiparallel (tetramer) quadruplex exhibited by the double repeat of the human telomere.
  63. (2005). Prevalence of quadruplexes in the human genome.
  64. (1998). Principles of Physical Biochemistry, 3rd edn. Pearson/Prentice Hall, Upper Saddle River,
  65. (2006). Quadruplex Nucleic Acids.. Royal Society of Chemistry,
  66. (1988). Raman spectroscopy of Z-form poly[d(A-T)].poly[d(A-T)].
  67. (2005). Repeat instability: mechanisms of dynamic mutations.
  68. (1983). Salt-induced conformational transition of poly[d(A-T)] poly[d(A-T)].
  69. (1972). Salt-induced cooperative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly(dG-dC).
  70. (1992). Single-stranded nucleic acid helical secondary structure stabilized by ionic bonds: d(A +-G)10.
  71. (2002). Slipped-strand DNAs formed by long (CAG).(CTG) repeats: slipped-out repeats and slip-out junctions.
  72. (1993). Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex.
  73. (1990). Spectroscopic and calorimetric investigation on the DNA triplex formed by d(CTCTTCTTTCTTTTCTTTCTTCTC) and d(GAGAAGAAAGA) at acidic pH.
  74. (2008). Stability and kinetics of G-quadruplex structures.
  75. (1990). Stabilization of the Z’ form of poly(dGdC):poly(dGdC) in solution by multivalent ions relates to the ZII form in crystals.
  76. (1993). Structural polymorphism of d(GA.TC)n DNA sequences. Intramolecular and intermolecular associations of the individual strands.
  77. (1993). Structural studies of biological macromolecules using vibrational circular dichroism.
  78. (1972). Structure and circular dichroism of DNA in concentrated polymer solutions.
  79. (1994). Structure and stability of human telomeric sequence.
  80. (2006). Structure of the human telomere in K + solution: an intramolecular (3+1) G-quadruplex scaffold.
  81. (2008). Targeting DNA with triplex-forming oligonucleotides to modify gene sequence.
  82. (2008). Targeting telomeres and telomerase.
  83. (2001). Telomerase inhibitors based on quadruplex ligands selected by a fluorescence assay.
  84. (1984). Temperature-dependent reversible transition of poly(dCdG).poly(dCdG) in ethanolic and methanolic solutions.
  85. (1974). The B to A transition of DNA in solution.
  86. (2000). The i-motif in nucleic acids.
  87. (1987). The structure of an oligo(dA) oligo(dT) tract and its biological implications.
  88. (1981). The transitions between leftand right-handed forms of poly(dG-dC).
  89. (1996). The unusual X-form DNA in oligodeoxynucleotides: dependence of stability on the base sequence and length.
  90. (1985). Three-state diagram for DNA.
  91. (2007). Towards a better understanding of the unusual conformations of the alternating guanine-adenine repeat strands of DNA.
  92. (1991). Transitions of poly(dI-dC), poly(dI-methyl 5dC) and poly(dI-bromo 5dC) among and within the B-, Z-, A- and X-DNA families of conformations.
  93. (2005). Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentrations of potassium.
  94. (2001). Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr 3+ ions: VCD and AFM evidence of DNA condensation.
  95. (1987). Z form of poly d(A-T).poly d(A-T) in solution studied by CD and UV spectroscopies.

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.