Biopolym. Cell. 2017; 33(2):81-91.
Reviews
Dependence of DNA persistence length on ionic conditions
1Zarudnaya M. I., 1Potyahaylo A. L., 1Hovorun D. M.
- Institute of Molecular Biology and Genetics, NAS of Ukraine
150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
Abstract
DNA functioning requires both compaction for packaging into chromatin or virus particles and accessibility for looping to control gene expression. The persistence length (P), closely related to the bending rigidity of double-stranded DNA, is highly relevant to these processes. In spite of numerous experimental and theoretical studies, a general agreement on the dependence of DNA persistence length on salt concentration has not been established and clear understanding about the fundamental forces responsible for DNA stiffness is still lacking. Here we describe a dependence of P vs Na+ concentration based on several studies and discuss the impact of different factors, including DNA G- and A-tracts, on DNA persistence length.
Keywords: DNA, persistence length, effective diameter, G-tracts, A-tracts
Full text: (PDF, in English)
References
[2]
Vologodskii A, Cozzarelli N. Modeling of long-range electrostatic interactions in DNA. Biopolymers. 1995;35(3):289–96.
[4]
Brian AA, Frisch HL, Lerman LS. Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition. Biopolymers. 1981;20(6)1305–28.
[5]
Yarmola EG, Zarudnaya MI, Lazurkin YuS. Osmotic pressure of DNA solutions and effective diameter of the double helix. J Biomol Struct Dyn. 1985;2(5)981–93.
[6]
Nicolai T, Mandel M. Ionic strength dependence of the second virial coefficient of low molar mass DNA frag-ments in aqueous solutions. Macromolecules. 1989; 22(1)438–44.
[7]
Rybenkov VV, Cozzarelli NR, Vologodskii AV. Pro-ba-bility of DNA knotting and the effective diameter of the DNA double helix. Proc Natl Acad Sci USA. 1993; 90(11)5307–11.
[9]
Peters JP, James Maher L III. DNA curvature and flexibility in vitro and in vivo. Q Rev Biophys. 2010;43(1)23–63.
[10]
Savelyev A. Do monovalent mobile ions affect DNA's flexibility at high salt content? Phys Chem Chem Phys. 2012;14(7)2250–4.
[11]
Kam Z, Borochov N, Eisenberg H. Dependence of laser light scattering of DNA on NaCl concentration. Bio-polymers. 1981;20(12)2671–90.
[12]
Rizzo V, Schellman J. Flow dichroism of T7 DNA as a function of salt concentration. Biopolymers. 1981;20(10)2143–63.
[13]
Sobel ES, Harpst JA. Effects of Na+ on the persistence length and excluded volume of T7 bacteriophage DNA. Biopolymers. 1991;31(13)1559–64.
[14]
Porschke D. Persistence length and bending dyna-mics of DNA from electrooptical measurements at high salt concentrations. Biophys Chem. 1991; 40(2)169–79.
[15]
Baumann CG, Smith SB, Bloomfield VA, Bustamante C. Ionic effects on the elasticity of single DNA molecules. Proc Natl Acad Sci U S A. 1997; 94(12)6185–90.
[16]
Manning GS. A procedure for extracting persistence lengths from light-scattering data on intermediate molecular weight DNA. Biopolymers. 1981;20(8)1751–5.
[17]
Post CB. Excluded volume of an intermediate-molecular-weight DNA. A Monte Carlo analysis. Biopolymers. 1983;22(4)1087–96.
[18]
Borochov N, Eisenberg H, Kam Z. Dependence of DNA conformation on the concentration of salt. Biopolymers. 1981;20(1)231–5.
[19]
Stigter D. Interactions of highly charged colloidal cylinders with applications to double-stranded DNA. Biopoly-mers. 1977;16(7)1435–48.
[20]
Cairney KL, Harrington RE. Flow birefringence of T7 phage DNA: dependence on salt concentration. Biopoly-mers. 1982;21(5)923–34.
[21]
Maret G, Weill G. Magnetic birefringence study of the electrostatic and intrinsic persistence length of DNA. Bio-polymers. 1983;22(12)2727–44.
[22]
Geggier S, Kotlyar A, Vologodskii A. Temperature dependence of DNA persistence length. Nucleic Acids Res. 2011;39(4)1419–26.
[23]
Savelyev A, Papoian GA. Chemically accurate coarse graining of double-stranded DNA. Proc Natl Acad Sci U S A. 2010;107(47):20340–5.
[24]
Hagerman PJ. Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers. 1981;20(7):1503–35.
[25]
Odijk T. Polyelectrolytes near the rod limit. J. Polym. Sci. Polym. Phys. Ed. 1977;15(3)477–83.
[26]
Skolnick J, Fixman M. Electrostatic persistence length of a wormlike polyelectrolyte. Macromolecules. 1977;10(5)944–8.
[27]
Manning GS. The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force. Biophys J. 2006;91(10)3607–16.
[28]
Fixman M. The flexibility of polyelectrolyte mo-le-cu-les. J Chem Phys. 1982;76(12), 6346–53.
[29]
Le Bret M. Electrostatic contribution to the persistence length of a polyelectrolyte. J Chem Phys. 1982;76(12), 6243–55.
[30]
Savelyev A, Materese CK, Papoian GA. Is DNA's rigidity dominated by electrostatic or nonelectrostatic interac-tions? J Am Chem Soc. 2011;133(48) 19290–3.
[31]
Peters JP, Yelgaonkar SP, Srivatsan SG, Tor Y, James Maher L III. Mechanical properties of DNA-like polymers. Nucleic Acids Res. 2013;41(22)10593–604.
[32]
Peters JP, Mogil LS, McCauley MJ, Williams MC, James Maher L III. Mechanical properties of base-modified DNA are not strictly determined by base stacking or electrostatic interactions. Biophys J. 2014;107(2)448–59.
[34]
Lipfert J, Doniach S, Das R, Herschlag D. Understanding nucleic acid-ion interactions. Annu Rev Biochem. 2014;83,813–41.
[35]
Manning GS. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys. 1978;11(2)179–246.
[36]
Savelyev A, MacKerell AD Jr. Differential impact of the monovalent ions Li+, Na+, K+, and Rb+ on DNA con-formational properties. J Phys Chem Lett. 2015; 6(1)212–6.
[37]
Savelyev A, MacKerell AD Jr. Competition among Li+, Na+, K+, and Rb+ monovalent ions for DNA in molecu-lar dynamics simulations using the additive CHARMM36 and Drude polarizable force fields. J Phys Chem B. 2015;119(12) 4428–40.
[38]
Savelyev A, MacKerell AD Jr. Differential deformability of the DNA minor groove and altered BI/BII backbone conformational equilibrium by the monovalent ions Li+, Na+, K+, and Rb+ via water-mediated hydrogen bond-ing. J Chem Theory Comput. 2015;11(9)4473–85.
[39]
Gebala M, Giambaşu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D. Cation-anion interac-tions within the nucleic acid ion atmosphere revealed by ion counting. J Am Chem Soc. 2015;137(46)14705–15.
[40]
Gebala M, Bonilla S, Bisaria N, Herschlag D. Does cation size affect occupancy and electrostatic screening of the nucleic acid ion atmosphere? J Am Chem Soc. 2016;138(34)10925–34.
[41]
Geggier S, Vologodskii A. Sequence dependence of DNA bending rigidity. Proc Natl Acad Sci U S A. 2010;107(35)15421–26.
[42]
Ng H-L, Dickerson RE. Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG. Nucleic Acids Res. 2002;30(18)4061–7.
[43]
Gao YG, Robinson H, Wang AH. High-resolution A-DNA crystal structures of d(AGGGGCCCCT). An A-DNA model of poly(dG) x poly(dC). Eur J Biochem. 1999;261(2)413–20.
[44]
Dornberger U, Spacková N, Walter A, Gollmick FA, Sponer J, Fritzsche H. Solution structure of the dodecamer d-(CATGGGCCCATG)2 is B-DNA. Experimental and molecular dynamics study. J Biomol Struct Dyn. 2001;19(1)159–74.
[45]
Lindqvist M, Gräslund A. An FTIR and CD study of the structural effects of G-tract length and sequence context on DNA conformation in solution. J Mol Biol. 2001; 314(3)423–32.
[46]
Trantírek L, Štefl R, Vorlíčková M, Koča J, Sklenár V, Kypr J. An A-type double helix of DNA having B-type puckering of the deoxyribose rings. J Mol Biol. 2000; 297(4)907–22.
[47]
Štefl R, Trantírek L, Vorličková M, Koča J, Sklenár V, Kypr J. A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC). J Mol Biol. 2001;307(2):513–24.
[48]
Haran TE, Mohanty U. The unique structure of A-tracts and intrinsic DNA bending. Q Rev Biophys. 2009;42(1)41–81.
[49]
Hovorun DM. On the microstructural origin of the linear DNA curvature. Dopov Nac Acad Nauk Ukr. 1998;5:189–95.
[50]
Ghosh A, Bansal M. C-H.O hydrogen bonds in minor groove of A-tracts in DNA double helices. J Mol Biol. 1999;294(5)1149–58.
[51]
Munksgaard Nielsen L, Holm AI, Varsano D, Kadhane U, Hoffmann SV, Di Felice R, Rubio A, Brøndsted Niel-sen S. Fingerprints of bonding motifs in DNA duplexes of adenine and thymine revealed from circular dichroism: synchrotron radiation experiments and TDDFT calculations. J Phys Chem B. 2009;113(28)9614–9.
[52]
Premilat S, Albiser G. X-ray fibre diffraction study of an elevated temperature structure of poly(dA)•poly(dT). J Mol Biol. 1997;274(1)64–71.
[53]
Zubatiuk T, Shishkin O, Gorb L, Hovorun D, Leszczynski J. Structural waters in the minor and major grooves of DNA – a major factor governing structural adjustments of the A-T mini-helix. J Phys Chem B. 2015;119(2)381–91.
[54]
Stellwagen E, Peters JP, James Maher L III, Stellwagen NC. DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations. Biochemistry. 2013;52(24)4138–48.
[55]
Stellwagen E, Dong Q, Stellwagen NC. Flanking A•T basepairs destabilize the B* conformation of DNA A-tracts. Biophys J. 2015;108(9)2291–9.
