DNA; G-quadruplex; kinetics; guanine; modified bases; mass spectrometry
Abstract :
[en] Parallel tetramolecular quadruplexes may be formed with short oligodeoxynucleotides bearing a block of three or more guanines. We analyze the properties of sequence variants of parallel quadruplexes in which each guanine of the central block was systematically substituted with a different base. Twelve types of substitutions were assessed in more than 100 different sequences. We conducted a comparative kinetic analysis of all tetramers. Electrospray mass spectrometry was used to count the number of inner cations, which is an indicator of the number of effective tetrads. In general, the presence of a single substitution has a strong deleterious impact on quadruplex stability, resulting in reduced quadruplex lifetime/ thermal stability and in decreased association rate constants. We demonstrate extremely large differences in the association rate constants of these quadruplexes depending on modification position and type. These results demonstrate that most guanine substitutions are deleterious to tetramolecular quadruplex structure. Despite the presence of well- defined non- guanine base quartets in a number of NMR and X- ray structures, our data suggest that most non- guanine quartets do not participate favorably in structural stability, and that these quartets are formed only by virtue of the docking platform provided by neighboring G- quartets. Two notable exceptions were found with 8- bromoguanine ( X) and 6- methyl- isoxanthopterin ( P) substitutions, which accelerate quadruplex formation by a factor of 10 when present at the 50 end. The thermodynamic and kinetic data compiled here are highly valuable for the design of DNA quadruplex assemblies with tunable association/ dissociation properties.
Neidle,S. and Parkinson,G.N. (2003) The structure of telomeric DNA. Curr. Opin. Struct. Biol., 13, 275-283.
Burge,S., Parkinson,G.N., Hazel,P., Todd,A.K. and Neidle,S. (2006) Quadruplex DNA: Sequence, topology and structure. Nucleic Acids Res. 34, 5402-5415.
Gellert,M., Lipsett,M.N. and Davies,D.R. (1962) Helix formation by guanylic acid. Proc. Natl. Acad. Sci. USA, 48, 2013-2018.
Grand,C.L., Powell,T.J., Nagle,R.B., Bearss,D.J., Tye,D., Gleason-Guzman,M. and Hurley,L.H. (2004) Mutations in the G-quadruplex silencer element and their relationship to c-MYC overexpression, NM23 repression, and therapeutic rescue. Proc. Natl. Acad. Sci. USA, 101, 6140-6145.
Schaffitzel,C., Berger,I., Postberg,J., Hanes,J., Lipps,H.J. and Plückthun,A. (2001) In vitro generated antibodies specific for telomeric guanine quadruplex DNA react with Stylonychia lemnae macronuclei. Proc. Natl. Acad. Sci. USA, 98, 8572-8577.
Duquette,M.L., Handa,P., Vincent,J.A., Taylor,A.F. and Maizels,N. (2004) Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. Genes Dev., 18, 1618-1629.
Paeschke,K., Simonsson,T., Postberg,J., Rhodes,D. and Lipps,H. (2005) Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nat. Struct. Mol. Biol., 12, 847-854.
Davis,J.T. (2004) G-quartets 40 years later: From 5′-GMP to molecular biology and supramolecular chemistry. Angew. Chem. Int. Ed., 43 668-698.
Alberti,P., Bourdoncle,A., Saccà,B., Lacroix,L. and Mergny,J.L. (2006) DNA nanomachines and nanostructures involving quadruplexes. Org. Biomol. Chem., 4, 3383-3391.
Maizels,N. (2006) Dynamic roles for G4 DNA in the biology of eukaryotic cells. Nature Struct. Mol. Biol., 13, 1055-1059.
Oganesian,L. and Bryan,T.M. (2007) Physiological relevance of telomeric G-quadruplex formation: A potential drug target. Bioessays, 29 155-165.
Spackova,N., Berger,I. and Sponer,J. (1999) Nanoseconds molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules. J. Am. Chem. Soc., 121, 5519-5534.
Stefl,R., Cheatham,T.E., Spackova,N., Fadrna,E., Berger,I., Koca,J. and Sponer,J. (2003) Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophys. J., 85, 1787-1804.
Wyatt,J.R., Davis,P.W. and Freier,S.M. (1996) Kinetics of Gquartet-mediated tetramer formation. Biochemistry, 35, 8002-8008.
Mergny,J.L., De Cian,A., Ghelab,A., Saccà,B. and Lacroix,L. (2005) Kinetics of tetramolecular quadruplexes. Nucleic Acids Res., 33 81-94.
Mergny,J.L., De Cian,A., Amrane,S. and Webba da Silva,M. (2006) Kinetics of double-chain reversals bridging contiguous quartets in tetramolecular quadruplexes. Nucleic Acids Res., 34, 2386-2397.
Petraccone,L., Pagano,B., Esposito,V., Randazzo,A., Piccialli,G., Barone,G., Mattia,C.A. and Giancola,C. (2005) Thermodynamics and kinetics of PNA-DNA quadruplex-forming chimeras. J. Am. Chem. Soc. 127, 16215-16223.
Esposito,V., Randazzo,A., Piccialli,G., Petraccone,L., Giancola,C. and Mayol,L. (2004) Effects of an 8-bromodeoxyguanosine incorporation on the parallel quadruplex structure [d(TGGGT)](4). Org. Biomol. Chem., 2, 313-318.
Petraccone,L., Erra,E., Esposito,V., Randazzo,A., Galeone,A., Barone,G. and Giancola,C. (2005) Biophysical properties of quadruple helices of modified human telomeric DNA. Biopolymers, 77, 75-85.
Patel,P.K. and Hosur,R.V. (1999) NMR observation of T-tetrads in a parallel stranded DNA quadruplex formed by Saccharomyces cerevisiae telomere repeats. Nucleic Acid Res., 27, 2457-2464.
Patel,P.K., Bhavesh,N.S. and Hosur,R.V. (2000) NMR observation of a novel C-tetrad in the structure of the SV40 repeat sequence GGGCGG. Biochem. Biophys. Res. Commun., 270, 967-971.
Pan,B.C., Xiong,Y., Shi,K., Deng,J.P. and Sundaralingam,M. (2003) Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: Implications for specific binding in RNA tetraplexes. Structure, 11, 815-823.
Cheong,C.J. and Moore,P.B. (1992) Solution structure of an unusually stable RNA tetraplex containing G-quartet and U-quartet structures. Biochemistry, 31, 8406-8414.
Pan,B.C., Xiong,Y., Shi,K. and Sundaralingam,M. (2003) Crystal structure of a bulged RNA tetraplex at 1.1 angstrom resolution: Implications for a novel binding site in RNA tetraplex. Structure, 11, 1423-1430.
Driscoll,S.L., Hawkins,M.E., Balis,F.M., Pfleiderer,W. and Laws,W.R. (1997) Fluorescence properties of a new guanosine analog incorporated into small oligonucleotides. Biophys. J., 73, 3277-3286.
Hawkins,M.E., Pfleiderer,W., Balis,F.M., Porter,D. and Knutson,J.R. (1997) Fluorescence properties of pteridine nucleoside analogs as monomers and incorporated into oligonucleotides. Anal. Biochem., 244, 86-95.
Kejnovska,I., Kypr,J. and Vorlickova,M. (2007) Oligo(dT) is not a correct native PAGE marker for single-stranded DNA. Biochem. Biophys. Res. Commun., 353, 776-779.
Rosu,F., Gabelica,V., Houssier,C., Colson,P. and De Pauw,E. (2002) Triplex and quadruplex DNA structures studied by electrospray mass spectrometry. Rapid Commun. Mass Spectrom., 16, 1729-1736.
Rosu,F., Gabelica,V., Shin-ya,K. and DePauw,E. (2003) Telomestatin induced stabilization of the human telomeric DNA quadruplex monitored by electrospray mass spectrometry. Chem. Commun., 34, 2702-2703.
Lieberman,D.V. and Hardin,C.C. (2004) Extraction of information on the buildup and consumption of reactive intermediates from quadruplex DNA assembly time courses. Biochim. Biophysica. Acta, 1679, 59-64.
Mergny,J.L., Phan,A.T. and Lacroix,L. (1998) Following G-quartet formation by UV-spectroscopy. FEBS Lett., 435, 74-78.
Mergny,J.L., Li,J., Lacroix,L., Amrane,S. and Chaires,J.B. (2005) Thermal difference spectra: A specific signature for nucleic acid structures. Nucleic Acids Res., 33, e138.
Petraccone,L., Erra,E., Randazzo,A. and Giancola,C. (2006) Energetic aspects of locked nucleic acids quadruplex association and dissociation. Biopolymers, 83, 584-594.
Wallimann,P., Kennedy,R.J., Miller,J.S., Shalango,W. and Kenp,D.S. (2003) Dual wavelength parametric test of two-state models for circular dichroism spectra of helical polypeptides: Anomalous dichroic properties of alanine-rich peptides. J. Am. Chem. Soc., 125, 1203-1220.
Myers,J.C., Moore,S.A. and Shamoo,Y. (2003) Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isox-anthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures. J. Biol. Chem., 278, 42300-42306.
Saccà,B., Lacroix,L. and Mergny,J.L. (2005) The effect of chemical modifications on the thermal stability of different G-quadruplexes-forming oligonucleotides. Nucleic Acids Res., 33 1182-1192.
Pörschke,D. and Eigen,M. (1971) Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic - oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J. Mol. Biol., 62 361-381.
Rougée,M., Faucon,B., Mergny,J.L., Barcelo,F., Giovannangeli,C., Garestier,T. and Hélène,C. (1992) Kinetics and thermodynamics of triple-helix formation: Effects of ionic strength and mismatches. Biochemistry, 31, 9269-9278.
Alberti,P., Arimondo,P.B., Mergny,J.L., Garestier,T., Hélène,C. and Sun,J.S. (2002) A directional nucleation-zipping mechanism for triple-helix formation. Nucleic Acids Res., 30, 5407-5415.
Dias,E., Battiste,J.L. and Williamson,J.R. (1994) Chemical probe for glycosidic conformation in telomeric DNAs. J. Am. Chem. Soc., 116, 4479-4480.
Wang,Y. and Patel,D.J. (1994) Solution structure of the Tetrahymena telomeric repeat d(T(2)G(4))(4) G-tetraplex. Structure, 2, 1141-1156.
Zhang,N., Phan,A.T. and Patel,D.J. (2005) (3 + 1) Assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex. J. Am. Chem. Soc., 127, 17277-17285.
Dai,J.X., Dexheimer,T.S., Chen,D., Carver,M., Ambrus,A., Jones,R.A. and Yang,D.Z. (2006) An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution. J. Am. Chem. Soc., 128, 1096-1098.
Ambrus,A., Chen,D., Dai,J., Bialis,T., Jones,R.A. and Yang,D. (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res., 34, 2723-2735.
Luu,K.N., Phan,A.T., Kuryavyi,V., Lacroix,L. and Patel,D.J. (2006) Structure of the human telomere in K+ Solution: An intramolecular (3+1) G-quadruplex scaffold. J. Am. Chem. Soc., 128, 9963-9970.
Phan,A.T., Luu,K.N. and Patel,D.J. (2006) Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K+ solution. Nucleic Acids Res., 34, 5715-5719.
Mergny,J.L., Gros,J., De Cian,A., Bourdoncle,A., Rosu,F., Saccà,B., Guittat,L., Amrane,S., Mills,M. et al. (2006). Neidle,S. and Balasubramanian,S. (eds), Quadruplex Nucleic Acids, Cambridge, UK, RSC, pp. 31-80.
Stefl,R., Spackova,N., Berger,I., Koca,J. and Sponer,J. (2001) Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. Biophys. J., 80, 455-468.
Lopez de la Osa,J., Gonzalez,C., Gargallo,R., Rueda,M., Cubero,E., Orozco,M., Avino,A. and Eritja,R. (2006) Destabilization of quadruplex DNA by 8-aminoguanine. Chembiochem., 7, 46-48.
