Biopolym. Cell. 2011; 27(1):3-16.
Protein-DNA complexes: specificity and DNA readout mechanisms
1Boryskina O. P., 1Tkachenko M. Yu., 1Shestopalova A. V.
  1. O. Ya. Usikov Institute for Radio Physics and Electronics NAS of Ukraine
    12, Akademika Proskury Str., Kharkiv, Ukraine, 61085


Protein-nucleic acid recognition is essential in a number of cellular processes, in particular, gene regulation, DNA replication and compaction. Studies on the recognition mechanisms show that DNA sequence carries information which is read out by proteins that selectively bind to specific DNA sites. The review is focused on the processes taking place during formation of specific and nonspecific complexes of proteins and DNA. Special attention is paid to direct and indirect mechanisms of sequence-specific recognition. Several examples of protein-nucleic acid complexes are given to illustrate the variety of recognition mechanisms
Keywords: protein-nucleic acid complexes, specificity of protein-nucleic acid interaction, mechanisms of direct and indirect readout


[1] von Hippel P. H. Proteine-DNA recognition: new perspectives and underlying themes Science 1994 263, N 5148:769–770.
[2] Murphy F., Churchill M. Nonsequence-specific DNA recognition: a structural perspective Structure 2000 8, N 4:R83–R89.
[3] Luger K., Mader A., Richmond R., Sargent D., Richmond T. Crystal structure of the nucleosome core particle at 2.8 C resolution Nature 1997 389, N 6648:251–260.
[4] Yeh C., Chen F., Wang J., Cheng T., Hwang M., Tzou W. Directional shape complementarity at the proteine-DNA interface J. Mol. Recognit 2003 16, N 4:213–222.
[5] Benos P., Lapedes A., Stormo G. Is there a code for proteinDNA recognition? Probab(ilistical)ly... Bioessays 2002 24, N 5:466–475.
[6] Rhodes D., Schwabe J. W., Chapman L., Fairall L. Towards an understanding of protein-DNA recognition Phil. Trans. R. Soc. Lond. B. Biol. Sci 1996 351, N 1339:501–509.
[7] Oda M., Nakamura H. Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition Genes Cells 2000 5, N 5:319–326.
[8] Privalov P. L. Thermodynamic problems in structural molecular biology Pure Appl. Chem 2007 79, N 8:1445– 1462.
[9] Jen-Jacobson L., Engler L., Ames J., Kurpiewski M., Grigorescu A. Thermodynamic parameters of specific and nonspecific protein-DNA binding Supramol. Chem 2000 12, N 2:143–160.
[10] Spolar R. S., Record M. T. Jr. Coupling of local folding to site-specific binding of proteins to DNA Science 1994 263, N 5148:777–784.
[11] Liu Ch. C., Richard A. J., Datta K., LiCata V. J. Prevalence of temperature-dependent heat capacity changes in proteinDNA interactions Biophys. J 2008 94, N 8:3258– 3265.
[12] Kalodimos C. G., Biris N., Bonvin A. M., Levandoski M. M., Guennuegues M., Boelens R., Kaptein R. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes Science 2004 305, N 5682:386–389.
[13] Rohs R., Jin X., West S., Joshi R., Honig B., Mann R. Origins of specificity in protein-DNA recognition Annu. Rev. Biochem 2010 79:233–269.
[14] Luscombe N. M., Austin S. E., Berman H. M., Thornton J. M. An overview of the structures of protein-DNA complexes Genome Biol 2000 1, N 1 r001.1–r001.10.
[15] Garvie C. W., Wolberger C. Recognition of specific DNA sequences Mol. Cell 2001 8, N 5:937–946.
[16] Krishna S. S., Majumdar I., Grishin N. V. Structural classification of zinc fingers: survey and summary Nucl. Acids Res 2003 31, N 2:532–550.
[17] Pingoud A., Fuxreiter M., Pingoud V., Wende W. Type II restriction endonucleases: structure and mechanism Cell. Mol. Life Sci 2005 62, N 6:685–707.
[18] Contreras-Moreira B., Sancho J., Angarica V. E. Comparison of DNA binding across protein superfamilies Proteins 2010 78, N 1:52–62.
[19] Olson W. K., Gorin A. A., Lu X. J., Hock L. M., Zhurkin V. B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes Proc. Natl Acad. Sci. USA 1998 95, N 19:11163–11168.
[20] Jones S., van Heyningen P., Berman H. M., Thornton J. M. Protein-DNA interactions: a structural analysis J. Mol. Biol 1999 287, N 5:877–896.
[21] Koudelka G. B., Mauro S. A., Ciubotaru M. Indirect readout of DNA sequence by proteins: the roles of DNA sequence-dependent intrinsic and extrinsic forces Prog. Nucl. Acids Res. Mol. Biol 2006 81, N 1:143–177.
[22] Locasale J. W., Napoli A. A., Chen S., Berman H. M., Lawson C. L. Signatures of protein-DNA recognition in free DNA binding sites J. Mol. Biol 2009 386, N 4:1054–1065.
[23] Ladbury J. E., Wright J. G., Sturtevant J. M., Sigler P. B. A thermodynamic study of the Trp repressor-operator interaction J. Mol. Biol 1994 238, N 5:669–681.
[24] Seeman N. C., Rosenberg J. M., Rich A. Sequence-specific recognition of double helical nucleic acids by proteins Proc. Natl Acad. Sci. USA 1976 73, N 3:804–808.
[25] Gromiha M., Siebers J. G., Selvaraj S., Kono H., Sarai A. Intermolecular and intramolecular readout mechanisms in protein-DNA recognition J. Mol. Biol 2004 337, N 2:285–294.
[26] Sarai A., Kono H. Protein-DNA recognition patterns and predictions Annu. Rev. Biophys. Biomol. Struct 2005 34:379–398.
[27] Matthews B. W. Protein-DNA interaction. No code for recognition Nature 1988 335, N 6188:294–295.
[28] Coulocheri S. A., Pigis D. G., Papavassiliou K. A., Papavassiliou A. G. Hydrogen bonds in protein-DNA complexes: where geometry meets plasticity Biochimie 2007 89, N 11:1291–1303.
[29] Aeling K., Opel M., Steffen N., Tretyachenko-Ladokhina V., Hatfield G., Lathrop R., Senear D. Indirect recognition in sequence-specific DNA binding by E. coli integration host factor: the role of DNA deformation energy J. Biol. Chem 2006 281, N 51:39236–39248.
[30] Paillard G., Lavery R. Analyzing protein-DNA recognition mechanisms Structure 2004 12, N 1:113–122.
[31] Ohndorf U. M., Rould M. A., He Q., Pabo C. O., Lippard S. J. Basis for recognition of cisplatin-modified DNA by highmobility-group proteins Nature 1999 399, N 6737:708–712.
[32] Grosschedl R., Giese K., Pagel J. HMG domain proteins: architectural elements in the assembly of nucleoprotein structures Trends Genet 1994 10, N 3:94–100.
[33] Bewley C. A., Gronenborn A. M., Clore G. M. Minor groovebinding architectural proteins: structure, function, and DNA recognition Annu. Rev. Biophys. Biomol. Struct 1998 27:105–131.
[34] Rohs R., West S. M., Sosinsky A., Liu P., Mann R. S., Honig B. The role of DNA shape in protein-DNA recognition Nature 2009 461, N 7268:1248–1253.
[35] Kopka M. L., Lavelle L., Han G. W., Ng H. L., Dickerson R. E. An unusual sugar conformation in the structure of an RNA/ DNA decamer of the polypurine tract may affect recognition by RNase H J. Mol. Biol 2003 334, N 4:653–665.
[36] Zhang Y., Xi Z., Hegde R. S., Shakked Z., Crothers D. M. Predicting indirect readout effects in protein-DNA interactions Proc. Natl Acad. Sci. USA 2004 101, N 22:8337–8341.
[37] Watkins D., Mohan S., Koudelka G. B., Williams L. D. Sequence recognition of DNA by protein-induced conformational transitions J. Mol. Biol 2010 396, N 4:1145–1164.
[38] Otwinowski Z., Schevitz R. W., Zhang R. G., Lawson C. L., Joachimiak A., Marmorstein R. Q., Luisi B. F., Sigler P. B. Crystal structure of trp repressor/operator complex at atomic resolution Nature 1988 335, N 6188:321–329.
[39] Gowers D. M., Wilson G. G., Halford S. E. Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA Proc. Natl Acad. Sci. USA 2005 102, N 44:15883–15888.
[40] Hu T., Grosberg A. Y., Shklovskii B. I. How proteins search for their specific sites on DNA: the role of DNA conformation Biophys. J 2006 90, N 8:2731–2744.
[41] Ferreiro D. U., Sanchez I. E., de Prat Gay G. Transition state for protein-DNA recognition Proc. Natl Acad. Sci. USA 2008 105, N 31:10797–10802.
[42] Halford S. E. An end to 40 years of mistakes in DNA-protein association kinetics? Biochem. Soc. Trans 2009 37, pt 2:343–348.
[43] Lejeune D., Delsaux N., Charloteaux B., Thomas A., Brasseur R. Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure Proteins 2005 61, N 2:258–271.
[44] Buck M., Karplus M. Hydrogen bond energetics: a simulation and statistical analysis of N-methyl acetamide (NMA), water, and human lysozyme J. Phys. Chem. B 2001 105, N 44 :11000–11015.
[45] Luscombe N. M., Lascowski R. A., Thornton J. M. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level Nucl. Acids Res 2001 29, N 13:2860–2874.
[46] Mandel-Gutfreund Y., Schueler O., Margalit H. Comprehensive analysis of hydrogen bonds in regulatory protein DNAcomplexes: in search of common principles J. Mol. Biol 1995 253, N 2:370–382.
[47] Suzuki M. A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules Structure 1994 2, N 4:317–326.
[48] Mandel-Gutfreund Y., Margalit H., Jernigan R. L., Zhurkin V. B. A role for CH...O interactions in protein-DNA recognition J. Mol. Biol 1998 277, N 5:1129–1140.
[49] Mandel-Gutfreund Y., Margalit H. Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites Nucl. Acids Res 1998 26, N 10:2306–2312.
[50] Treger M., Westhof E. Statistical analysis of atomic contacts at RNA-protein interfaces J. Mol. Recognit 2001 14, N 4:199–214.
[51] Biot C., Wintjens R., Rooman M. Stair motifs at protein-DNA interfaces: nonadditivity of H-bond, stacking, and cation-interactions J. Am. Chem. Soc 2004 126, N 20:6220– 6221.
[52] Rooman M., Lievin J., Buisine E., Wintjens R. Cation-/Hbond stair motifs at protein-DNA interfaces J. Mol. Biol 2002 319, N 1:67–76.
[53] Tolstorukov M. Y., Jernigan R. L., Zhurkin V. B. Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching J. Mol. Biol 2004 337, N 1:65–76.
[54] Zhang Z., Gong Y., Guo L., Jiang T., Huang L. Structural insights into the interaction of the crenarchaeal chromatin protein Cren7 with DNA Mol. Microbiol 2010 76, N 3:749–759.
[55] Drozdov-Tikhomirov L. N., Linde D. M., Poroikov V. V., Alexandrov A. A., Skurida G. I. Molecular mechanisms of protein-protein recognition: whether the surface placed charged residues determine the recognition process J. Biomol. Struct. Dyn 2001 19, N 2:279–284.
[56] Norberg J. Association of protein-DNA recognition complexes: electrostatic and nonelectrostatic effects Arch. Biochem. Biophys 2003 410, N 1:48–68.
[57] Gurlie R., Duong T. H., Zakrzewska K. The role of DNA-protein salt bridges in molecular recognition: a model study Biopolymers 1999 49, N 4:313–327.
[58] Saecker R. M., Record M. T. Jr. Protein surface salt bridges and paths for DNA wrapping Curr. Opin. Struct. Biol 2002 12, N 3:311–319.
[59] Torrado M., Revuelta J., Gonzalez C., Corzana F., Bastida A., Asensio J. L. Role of conserved salt bridges in homeodomain stability and DNA binding J. Biol. Chem 2009 284, N 35:23765–23779.
[60] Spyrakis F., Cozzini P., Bertoli C., Marabotti A., Kellogg G., Mozzarelli A. Energetics of the protein-DNA-water interaction BMC Struct. Biol 2007 7:4–21.
[61] Giese K., Amsterdam A., Grosschedl R. DNA-binding properties of the HMG-domain of the lymphoid-specific transcriptional regulator LEF-1 Genes Dev 1991 5, N 12B:2567–2578.
[62] Watkins D., Hsiao C., Woods K. K., Koudelka G. B., Williams L. D. P22 c2 repressor-operator complex: mechanisms of direct and indirect readout Biochemistry 2008 47, N 8:2325–2338.
[63] Becker N. B., Wolff L., Everaers R. Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials Nucl. Acids Res 2006 34, N 19:5638–5649.
[64] Hud N. V., Plavec J. A unified model for the origin of DNA sequence-directed curvature Biopolymers 2003 69, N 1:144–158.
[65] Hays F. A., Teegarden A., Jones Z. J., Harms M., Raup D., Watson J., Cavaliere E., Ho P. S. How sequence defines structure: a crystallographic map of DNA structure and conformation Proc. Natl Acad. Sci. USA 2005 102, N 20:7157–7162.
[66] Svozil D., Kalina J., Omelka M., Schneider B. DNA conformations and their sequence preferences Nucl. Acids Res 2008 36, N 11:3690–3706.
[67] Boryskina O. P., Tkachenko M. Yu., Shestopalova A. V. Variability of DNA structure and protein-nucleic acid reconginition Biopolym. Cell 2010 26, N 5:360–372.
[68] Vargason J. M., Henderson K., Ho P. S. A crystallographic map of the transition from B-DNA to A-DNA Proc. Natl Acad. Sci. USA 2001 98, N 13:7265–7270.
[69] Dickerson R. E., Ng H. L. DNA structure from A to B Proc. Natl Acad. Sci. USA 2001 98, N 13:6986–6988.
[70] Wu L., Koudelka G. B. Sequence-dependent differences in DNA structure influence the affinity of P22 operator for P22 repressor J. Biol. Chem 1993 268, N 25:18975–18981.
[71] Weston S. A., Lahm A., Suck D. X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 C resolution J. Mol. Biol 1992 226, N 4:1237–1256.
[72] Heinemann U., Alings C., Bansal M. Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA EMBO J 1992 11, N 5:1931–1939.
[73] Wahl M. C., Sundaralingam M. Crystal structures of A-DNA duplexes Biopolymers 1997 44, N 1:45–63.
[74] Samanta S., Chakrabarti J., Bhattacharya D. Changes in thermodynamic properties of DNA base pairs in proteinDNA recognition J. Biomol. Struct. Dyn 2010 27, N 4:429–442.
[75] Arnott S., Hukins D. W. Optimised parameters for A-DNA and B-DNA Biochem. Biophys. Res. Communs 1972 47, N 6:1504–1509.
[76] Woods K. K., Lan T., McLaughlin L. W., Williams L. D. The role of minor groove functional groups in DNA hydration Nucl. Acids Res 2003 31, N 5:1536–1540.
[77] Haran T. E., Mohanty U. The unique structure of A-tracts and intrinsic DNA bending Q. Rev. Biophys 2009 42, N 1:41–81.
[78] Perez-Martin J., Rojo F., de Lorenzo V. Promoters responsive to DNA bending: a common theme in prokaryotic gene expression Microbiol. Rev 1994 58, N 2:268–290.
[79] Hagerman P. J. Sequence-directed curvature of DNA Annu. Rev. Biochem 1990 59:755–781.
[80] Gimenes F., Takeda K. I., Fiorini A., Gouveia F. S., Fernandez M. A. Intrinsically bent DNA in replication origins and gene promoters Genet. Mol. Res 2008 7, N 2:549– 558.
[81] Olson W. K., Bansal M., Burley S. K., Dickerson R. E., Gerstein M., Harvey S. C., Heinemann U., Lu X. J., Neidle S., Shakked Z., Sklenar H., Suzuki M., Tung C. S., Westhof E., Wolberger C., Berman H. M. A standard reference frame for the description of nucleic acid base-pair geometry J. Mol. Biol 2001 313, N 1:229–237.
[82] Lankas F., Sponer J., Langowski J., Cheatham T. E. 3rd. DNA basepair step deformability inferred from molecular dynamics simulations Biophys. J 2003 85, N 5:2872– 2883.
[83] Fujii S., Kono H., Takenaka S., Go N., Sarai A. Sequencedependent DNA deformability studied using molecular dynamics simulations Nucl. Acids Res 2007 35, N 18:6063–6074.
[84] Beveridge D. L., Barreiro G., Byun K. S., Case D. A., Cheatham T. E. 3rd, Dixi S. B., Giudice E., Lankas F., Lavery R., Maddocks J. H., Osman R., Seibert E., Sklenar H., Stoll G., Thayer K. M., Varnai P., Young M. A. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps Biophys. J 2004 87, N 6:3799–3813.
[85] Chen Y., Kortemme T., Robertson T., Baker D., Varani G. A new hydrogen-bonding potential for the design of proteinRNA interactions predicts specific contacts and discriminates decoys Nucl. Acids Res 2004 32, N 17:5147–5162.
[86] Lavery R. Recognizing DNA Q. Rev. Biophys 2005 38, N 4:339–344.
[87] Temiz N. A., Camacho C. J. Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface Nucl. Acids Res 2009 37, N 12:4076–4088.
[88] Lu X., Olson W. K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucl. Acids Res 2003 31, N 17:5108–5121.
[89] Elrod-Erickson M., Rould M. A., Nekludova L., Pabo C. O. Zif268 protein-DNA complex refined at 1.6 C: a model system for understanding zinc finger-DNA interactions Structure 1996 4, N 10:1171–1180.
[90] Gamsjaeger R., Liew C. K., Loughlin F. E., Crossley M., Mackay J. P. Sticky fingers: zinc-fingers as protein-recognition motifs Trends Biochem. Sci 2007 32, N 2:63–70.
[91] Haran T. E., Joachimiak A., Sigler P. B. The DNA target of the trp repressor EMBO J 1992 11, N 8:3021–3030.
[92] Wellenzohn B., Flader W., Winger R. H., Hallbrucker A., Mayer E., Liedl K. R. Indirect readout of the trp-repressoroperator complex by B-DNA’s backbone conformation transitions Biochemistry 2002 41, N 12:4088–4095.
[93] Locasale J. W., Napoli A. A., Chen S., Berman H. M., Lawson C. L. Signatures of protein-DNA recognition in free DNA binding sites J. Mol. Biol 2009 386, N 4:1054–1065.
[94] Little E. J., Babic A. C., Horton N. C. Early interrogation and recognition of DNA sequence by indirect readout Structure 2008 16, N 12:1828–1837.
[95] Jurica M. S., Stoddart B. L. Homing endonucleases: structure, function and evolution Cell Mol. Life Sci 1999 55, N 10:1304–1326.
[96] Sidorova N. Y., Rau D. C. Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences Proc. Natl Acad. Sci. USA 1996 93, N 22:12272– 12277.
[97] Jayaram B., Jain T. The role of water in protein-DNA recognition Annu. Rev. Biophys. Biomol. Struct 2004 33:343–361.
[98] Viadiu H., Aggarwal A. K. The role of metals in catalysis by the restriction endonuclease BamHI Nat. Struct. Biol 1998 5, N 10:910–916.
[99] Selvaraj S., Kono H., Sarai A. Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/ asymmetric and cognate/non-cognate binding J. Mol. Biol 2002 322, N 5: 907–915.
[100] Richmond T. J., Davey C. A. The structure of DNA in the nucleosome core Nature 2003 423, N 6936:145–150.
[101] Davey C. A., Sargent D. F., Luger K., Maeder A. W., Richmond T. J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 C resolution J. Mol. Biol 2002 319, N 5:1097–1113.
[102] Tolstorukov M. Y., Colasanti A. V., McCandlish D. M., Olson W. K., Zhurkin V. B. A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning J. Mol. Biol 2007 371, N 3:725–738.
[103] Ong M. S., Richmond T. J., Davey C. A. DNA stretching and extreme kinking in the nucleosome core J. Mol. Biol 2007 368, N 4:1067–1074.
[104] Lundback T., Hansson H., Knapp S., Ladenstein R., Hard T. Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus J. Mol. Biol 1998 276, N 4: 775–786.
[105] McAfee J. G., Edmondson S. P., Zegar I., Shriver J. W. Equilibrium DNA binding of Sac7d protein from the hyperthermophile Sulfolobus acidocaldarius: fluorescence and circular dichroism studies Biochemistry 1996 35, N 13:4034–4045.
[106] Dunham S. U., Lippard S. J. DNA sequence context and protein composition modulate HMG-domain protein recognition of cisplatin-modified DNA Biochemistry 1997 36, N 38:11428–11436.
[107] Imamura T., Izumi H., Nagatani G., Ise T., Nomoto M., Iwamoto Y., Kohno K. Interaction with p53 enhances binding of cisplatin-modified DNA by high mobility group 1 protein J. Biol. Chem 2001 276, N 10:7534–7540.
[108] Wozniak K., Blasiak J. Recognition and repair of DNA-cisplatin adducts Acta Biochim. Pol 2002 49, N 3:583– 596.
[109] Waldmann T., Baack M., Richter N., Gruss C. Structure-specific binding of the proto-oncogene protein DEK to DNA Nucl. Acids Res 2003 31, N 23:7003–7010.
[110] Ashworth J., Baker D. Assessment of the optimization of affinity and specificity at protein–DNA interfaces Nucl. Acids Res 2009 37, N 10 e73.
[111] Tkachenko M. Y., Boryskina O. P., Shestopalova A. V., Tolstorukov M. Y. ProtNA-ASA: Protein-nucleic acid structural database with information on accessible surface area Int. J. Quant. Chem 2010 110, N 1:230–232.