Thermodynamic contributions of 5’- and 3’-single strand dangling-ends to the stability of short duplex DNAs

Abstract

Differential scanning calorimetry (DSC) melting analysis was performed on 27 short double stranded DNA duplexes containing 15 to 25 base pairs. Experimental duplexes were divided into two categories containing either two 5’ dangling-ends or one 5’ and one 3’ dangling-end. Duplex regions were incrementally reduced from 25 to 15 base pairs with a concurrent increase in length of dangling-ends from 1 to 10 bases. Blunt-ended duplexes from 15 to 25 base pairs served as controls. An additional set of molecules containing 21 base pair duplexes and a single four base dangling-end were also examined. DSC melting curves were measured in varying concentrations of sodium ion (Na+). From these measurements, thermodynamic parameters for 5’ and 3’ dangling-ends were evaluated as a function of dangling end length. 5’ ends were found to be slightly stabilizing but essentially constant while the 3’ ends were destabilizing with increasing length of the dangling-end. 3’ ends also display a stronger dependence on Na+ concentration. In lower Na+ environment, the 3’ ends were more destabilizing than in higher salt environment suggesting a more significant electrostatic component of the destabilizing interactions. Analysis of thermodynamic parameters of dangling ended duplexes as a function of Na+ concentration indicated the 3' dangling ends behave differently than 5' dangling ended and blunt-ended duplexes. Molecules with one 5' and one 3' dangling end showed variation in excess specific heat capacity (ΔCp) when compared to the blunt-ended molecule, while the molecules with two 5’ ends had ΔCp values that were essentially the same as blunt-ended duplexes. These observations suggested differences exist in duplexes with 3’ and 5’ dangling ends, which are interpreted in terms of composite differences in interactions with Na+, solvent, and terminal base pairs of the duplex.

Share and Cite:

Dickman, R. , Manyanga, F. , Brewood, G. , Fish, D. , Fish, C. , Summers, C. , Horne, M. and Benight, A. (2012) Thermodynamic contributions of 5’- and 3’-single strand dangling-ends to the stability of short duplex DNAs. Journal of Biophysical Chemistry, 3, 1-15. doi: 10.4236/jbpc.2012.31001.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] 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
[2] Rouzina, I. and Bloomfield, V.A. (1999) Heat capacity effects on the melting of DNA. 1. General aspects. Biophysical Journal, 77, 3242-3251. doi:10.1016/S0006-3495(99)77155-9
[3] Wu, P., Nakano, S. and Sugimoto, N. (2002) Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation. European Journal of Biochemistry, 269, 2821-2830. doi:10.1046/j.1432-1033.2002.02970.x
[4] Freier, S.M., Sugimoto, N., Sinclair, A., Alkema, D., Neilson, T., Kierzek, R., Caruthers, M.H. and Turner, D.H. (1986) Stability of XGCGCP, GCGCYP, and XGCGCYP helixes—An empirical estimate of the energetics of hydrogen-bonds in nucleic-acids. Biochemistry, 25, 3214-3219. doi:10.1021/bi00359a020
[5] SantaLucia, J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodyna- mics. Proceedings of the National Academy of Sciences of the United States of America, 95, 1460-1465. doi:10.1073/pnas.95.4.1460
[6] Owczarzy, R., You, Y., Moreira, B.G., Manthey, J.A., Huang, L.Y., Behlke, M.A. and Walder, J.A. (2004) Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures. Biochemistry, 43, 3537-3554. doi:10.1021/bi034621r
[7] Holbrook, J.A., Capp, M.W., Saecker, R.M. and Record, M.T. (1999) Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: Interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry, 38, 8409-8422. doi:10.1021/bi990043w
[8] Chalikian, T.V., Volker, J., Plum, G.E. and Breslauer, K.J. (1999) A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques. Proceedings of the National Academy of Sciences of the United States of America, 96, 7853-7858. doi:10.1073/pnas.96.14.7853
[9] Ohmichi, T., Nakano, S., Miyoshi, D. and Sugimoto, N. (2002) Long RNA dangling end has large energetic contribution to duplex stability. Journal of the American Chemical Society, 124, 10367-10372. doi:10.1021/ja0255406
[10] Senior, M., Jones, R.A. and Breslauer, K.J. (1988) Influence of dangling thymidine residues on the stability and structure of 2 dna duplexes. Biochemistry, 27, 3879-3885. doi:10.1021/bi00410a053
[11] Cantor, C.R., Warshaw, M.M. and Shapiro, H. (1970) Oli-gonucleotide Interactions III. Circular Dichroism Studies of the Conformation of Deoxyoligonucleotides. Biopolymers, 9, 1059-1077. doi:10.1002/bip.1970.360090909
[12] Cavaluzzi, M.J. and Borer, P.N. (2004) Revised UV extinction coefficients for nucleoside‐5’‐monophosphates and unpaired DNA and RNA. Nucleic Acids Research, 32, e13. doi:10.1093/nar/gnh015
[13] Bommarito, S., Peyret, N. and SantaLucia, J. (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Research, 28, 1929-1934. doi:10.1093/nar/28.9.1929
[14] 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) 2ggatac(t)4gtatcc-3’, where x, y = A, T, G, C. Biopolymers, 30, 829-845. doi:10.1002/bip.360300718
[15] Quartin, R.S. and Wetmur, J.G. (1989) Effect of ionic-strength on the hybridization of oligodeoxynucleotides with reduced charge due to methylphosphonate linkages to unmodified oligodeoxynucleotides containing the complementary sequence. Biochemistry, 28, 1040-1047. doi:10.1021/bi00429a018
[16] Riccelli, P.V., Mandell, K.E. and Benight, A.S. (2002) Melting studies of dangling-ended DNA hairpins: Effects of end length, loop sequence and biotinylation of loop bases. Nucleic Acids Research, 30, 4088-4093. doi:10.1093/nar/gkf514
[17] SantaLucia, J. and Hicks, D. (2004) The thermodynamics of DNA structural motifs. Annual Review of Biophysics and Biomolecular Structure, 33, 415-440. doi:10.1146/annurev.biophys.32.110601.141800
[18] Isaksson, J., Acharya, S., Barman, J., Cheruku, P. and Chattopadhyaya, J. (2004) Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations and show directional differences in stacking pattern. Biochemistry, 43, 15996-16010. doi:10.1021/bi048221v
[19] Isaksson, J. and Chattopadhyaya, J. (2005) A uniform mechanism correlating dangling-end stabilization and stacking geometry. Biochemistry, 44, 5390-5401. doi:10.1021/bi047414f
[20] Manning, G.S. and Mohanty, U. (1997) Counterion condensation on ionic oligomers. Physica A, 247, 196-204. doi:10.1016/S0378-4371(97)00413-5
[21] Sugimoto, N., Nakano, S., Yoneyama, M. and Honda, K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Research, 24, 4501-4505. doi:10.1093/nar/24.22.4501
[22] Manyanga, F., Horne, M.T., Brewood, G.P., Fish, D.J., Dickman, R. and Benight, A.S. (2009) Origins of the “nucleation” free energy in the hybridization thermodynamics of short duplex DNA. Journal of Physical Chemistry B, 113, 2556-2563. doi:10.1021/jp809541m
[23] Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31, 3406-3415. doi:10.1093/nar/gkg595

Journals Menu
Follow SCIRP
Contact us
+1 323-425-8868
customer@scirp.org
WhatsApp +86 18163351462(WhatsApp)
Click here to send a message to me 1655362766
Paper Publishing WeChat

Copyright © 2024 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.

  翻译：