A single base permutation in any loop of a folded intramolecular quadruplex influences its structure and stability


The human telomere sequence (TTAGGG)4 folds into an unusual conformation possessing three G-tetrads linked by TTA loops. The first loop is a propeller loop while the second and third loops are transverse loops. Using Circular Dichroism (CD) spectroscopy, we have investigated the effect of sequence context on the structures and stabilities of intramolecular G-quadruplexes related to the human telomere sequence by considering all permutations of T and A within the loops. The results indicate that changing only one base in any one loop can have a dramatic effect on the conformation of the quadruplex as well as its melting temperature, Tm. Thus, each sequence studied has a unique CD spectrum and Tm. In general, variants with a modified second loop are the most stable while the wild type sequence is the least stable. The observed difference in CD spectra and melting temperature are discussed in terms of base stacking within the loop and stacking of the loop bases with adjacent G-tetrads.

Share and Cite:

Yadav, D. and D. Sheardy, R. (2012) A single base permutation in any loop of a folded intramolecular quadruplex influences its structure and stability. Journal of Biophysical Chemistry, 3, 341-347. doi: 10.4236/jbpc.2012.34042.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Otokiti, E.O. and Sheardy, R.D. (1997) Sequence effects on the relative thermodynamic stabilities of B-Z junction forming DNA oligomers. Biophysical Journal, 73, 3135-3141. doi:10.1016/S0006-3495(97)78339-5
[2] Paiva, A.M. and Sheardy, R.D. (2004) The influence of sequence context and length on the structure and stability of triplet repeat DNA oligomers. Biochemistry, 43, 14218-14227. doi:10.1021/bi0494368
[3] Paiva, A.M. and Sheardy, R.D. (2005) The influence of sequence context and length on the kinetics of duplex formation from complementary hairpins possessing (CNG) repeats. Journal of the American Chemical Society, 127, 5581-5585. doi:10.1021/ja043783n
[4] Tucker, B.A., Gabriel, S. and Sheardy, R.D. (2012) A CD Spectroscopic Investigation of Inter- and Intramolecular DNA Quadruplexes. In: Sheardy, R.D. and Winkle, S.A., Eds, Frontiers in Nucleic Acids, ACS Symposium Books, Washington DC.
[5] Sen, D. and Gilbert, W. (1990) Sodium-potassium switch in the formation of four-stranded G4-DNA. Nature, 344, 410-414. doi:10.1038/344410a0
[6] Hardin, C.C., Henderson, E., Watson, T. and Prosser, J.K. (1991) Monovalent cation induced structural transitions in telomeric DNAs: G-DNA folding intermediates. Biochemistry, 30, 4460-4472. doi:10.1021/bi00232a013
[7] Gray, R.D., Li, J. and Chaires, J.B. (2009) Energetics and kinetics of a conformational switch in G-quadruplex DNA. Journal of Physical Chemistry B, 113, 2676-2683. doi:10.1021/jp809578f
[8] Gray, R.D. and Chaires, J.B. (2011) Linkage of cation binding and folding in human telomere quadruplex DNA. Biophysical Chemistry, 159, 205-209. doi:10.1016/j.bpc.2011.06.012
[9] Phan, A.T., Gueron, M. and Leroy, J.L. (2000) The solution structure and internal motions of a fragment of the cytidine-rich strand of the human telomere. Journal of Molecular Biology, 299, 123-144. doi:10.1006/jmbi.2000.3613
[10] Phan, A.T. and Mergny, J.-L. (2002) Human telomeric DNA: G-quadruplex, i-motif and Watson-Crick double helix. Nucleic Acids Research, 30, 4618-4625. doi:10.1093/nar/gkf597
[11] Kaushik, M., Suehl, N. and Marky, L.A. (2007) Calorimetric unfolding of the bimolecular and i-motif complexes of the human telomere complementary strand, d(C3TA2)4. Biophysical Chemistry, 126, 154-164. doi:10.1016/j.bpc.2006.05.031
[12] Choi, J., Kim, S., Tachikawa, T., Fujitsuka, M. and Majima. T. (2011) pH-induced intramolecular folding dynamics of i-motif DNA. Journal of the American Chemical Society, 133, 16146-16153. doi:10.1021/ja2061984
[13] Jin, K.S., Shin, S.R., Ahn, B., Rho, Y., Kim. S.J. and Ree, M. (2009) pH-dependent structures of an i-motif DNA in solution. Journal of Physical Chemistry, 113, 1852-1856. doi:10.1021/jp808186z
[14] Antonacci, C., Chaires, J.B. and Sheardy, R.D. (2007) Biophysical characterization of the human telomeric repeat (TTAGGG)4 in potassium solution. Biochemistry, 47, 4654-4660. doi:10.1021/bi602511p
[15] Hazel, P., Huppert, J., Balasubramanian, S. and Neidle, S. (2004) Loop-length-dependent folding of G-quadruk-plexes. Journal of the American Chemical Society, 126, 16405-16415. doi:10.1021/ja045154j
[16] Risitano, A. and Fox, K.R. (2004) Influence of loop size on the stability of intramolecular DNA quadruplexes. Nucleic Acids Research, 32, 2598-2606. doi:10.1093/nar/gkh598
[17] Rujan, I.N., Meleny, J.C. and Bolton, P.H. (2005) Vertebrate telomere repeat DNAs favor external loop propeller quadruplex structures in the presence of high concentration of potassium. Nucleic Acids Research, 33, 2022-2031. doi:10.1093/nar/gki345
[18] Kumar, N., Sahoo, B., Varun, K.A.S., Maiti, S. and Maiti, S. (2008) Effect of loop variation on quadruplex-Watson Crick duplex competition. Nucleic Acids Research, 36, 4433-4442. doi:10.1093/nar/gkn402
[19] Balkwill, G.D., Garner, T.P., Williams, H.E.L. and Searle, M.S. (2009) Folding topology of a bimolecular quadruplex containing a stable mini-hairpin motif within the diagonal loop. Journal of Molecular Biology, 385, 1600-1615. doi:10.1016/j.jmb.2008.11.050
[20] Fugimoto, T., Miyoshi, D., Tateishi-Karimata, H. and Sugimoto, N. (2009) Thermal stability and hydration state of DNA G-quadruplex regulated by loop regions. Nucleic Acids Symposium Series, 53, 237-238. doi:10.1093/nass/nrp119
[21] Gray, D.M., Wen, J.-D., Gray, C.W., Repges, R., Repges, C., Raabe, G. and Fleischhauer, J. (2008) Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities. Chirality, 20, 431-440. doi:10.1002/chir.20455
[22] Johnson, W.C. Jr. (1992) Analysis of circular dichroism spectra. Methods in Enzymology, 210, 426-447. doi:10.1016/0076-6879(92)10022-6
[23] Johnson, W.C. Jr. (2000) CD of nucleic acids. In: Borova, N., Naknishi, K. and Woody, R.W., Eds., Circular Dichroism, 2nd Edition, Wiley-VCH, New York, 703-718.
[24] Breslauer, K.J., Frank, R., Blocker, H. and Marky, L.A. (1986) Predicting DNA duplex stability from base sequence. Proceedings of the National Academy of Science USA, 83, 3746-3750. doi:10.1073/pnas.83.11.3746
[25] Doktycz, M.J., Goldstein, R.F., Paner, T.M., Gallo, F.J. and Benight, A.S. (1992) Studies of DNA dumbbells. I. melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: Evaluation of the nearest-neighbor stacking interactions in DNA. Biopolymers, 32, 849-864. doi:10.1002/bip.360320712
[26] Hunter, C.A. (1993) Sequence-dependent DNA structure: The role of base stacking interactions. Journal of Molecular Biology, 230, 1025-1054. doi:10.1006/jmbi.1993.1217
[27] Freidman, R.A. and Honig, B. (1995) A free energy analysis of nucleic acid base stacking in aqueous solution. Biophysical Journal, 69, 1528-1535. doi:10.1016/S0006-3495(95)80023-8
[28] SantaLucia, J. Jr., Allawi, H.T. and Seneviratne, P.A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry, 35, 3555-3562. doi:10.1021/bi951907q
[29] Senior, M.M., Jones, R.A. and Breslauer, K.J. (1988) Influence of loop residues on the relative stabilites of DNA hairpin structures. Proceedings of the National Academy of Science USA, 85, 6242-6246. doi:10.1073/pnas.85.17.6242
[30] Paner, T.M., Amaratunga, M., Doktycz, M.J. and Benight, A.S. (1990) Analysis of melting transitions of the DNA hairpins formed from oligomer sequences d[GGATA- (X)4GTATCC] (X = A, T, G, C). Biopolymers, 29, 1715-1734. doi:10.1002/bip.360291405
[31] Petersheim, M. and Turner, D.H. (1983) Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp and ACCGGUp. Biochemistry, 22, 256-263. doi:10.1021/bi00271a004
[32] Freier, S.M., Alkema, D., Sinclair, A. and Turner, D.H. (1985) Contributions of dangling end stacking and terminal base-pair formationto the stabilities of GGCCp, XCCGGp, XGGCCp and XCCGGY. Biochemistry, 24, 4533-4539. doi:10.1021/bi00338a008
[33] Senior, M.M., Jones, R.A. and Breslauer, K.J. (1988) Influence of dangling thymine residues on the stability and structure of two DNA duplexes. Biochemistry, 28, 720-725. doi:10.1002/bip.360300718
[34] Doktycz, M.J., Paner, T.M., Amaratunga, M. and Benight, A.S. (1990) Thermodynamic stability of the 5’ dangling-ended DNA hairpins formed from sequences 5’-(XY)2 GGATAC(T)4GTATCC-3’ where X,Y = A, T, G, C. Biopolymers, 30, 829-845.
[35] Marotta, S.P. and Sheardy, R.D. (1996) Conformational properties of Z-forming DNA oligomers bearing terminal unpaired bases. Biophysical Journal, 71, 3361-3369. doi:10.1016/S0006-3495(96)79529-2
[36] Bommarito, S., Peyret, N. and SantaLucia, J. Jr. (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Research, 28, 1929-1934. doi:10.1093/nar/28.9.1929
[37] Agatep, A., Fagbohan, O. and Sheardy, R.D. (2012) DNA Quadruplexes with Overhangs. Chancellor’s Symposium for Creative Arts and Research, Texas Woman’s University, Denton.
[38] Petraccone, L., Spink, C., Trent, J.O., Garbett, N.C., Mekmaysy, C.S., Giancola, C. and Chaires, J.B. (2011) Structure and stability of higher-order human telomeric quadruplexes. Journal of the American Chemical Society, 133, 20951-20961. doi:10.1021/ja209192a

Copyright © 2023 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.