Parallel-Stranded DNA with Natural Base Sequences

Molecular Biology

Volumn 37, Issue 2, 2003, Pages 223-231

  Shchyolkina, A K ^a   Borisova, O F ^a   Livshits, M A ^a   Jovin, T M ^b  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Biological role; Parallel stranded DNA; Structure; Thermodynamic parameters of formation

Indexed keywords

CYTOSINE DERIVATIVE; DNA; GUANINE DERIVATIVE; LIGAND; METHYL GROUP; MICROSATELLITE DNA; NUCLEOPROTEIN; NUCLEOTIDE; OLIGONUCLEOTIDE; PROTEIN; PROTON; SOLVENT;

BASE PAIRING; BIOLOGY; CELL FUNCTION; CHEMICAL COMPOSITION; CONFORMATION; DNA HELIX; DNA POLYMORPHISM; DNA STRAND; DNA STRUCTURE; DNA SYNTHESIS; ENERGY; ENTHALPY; GENE FUNCTION; GENE SEQUENCE; GENETIC STABILITY; GENOME; NUCLEOTIDE SEQUENCE; REVIEW; TELOMERE; THERMODYNAMICS; TRINUCLEOTIDE REPEAT; YEAST;

EID: 0037276353     PISSN: 00268933     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1023393521207     Document Type: Review

References (39)

1. Watson D., Crick F.H. 1953. A structure for deoxyribose nucleic acid. Nature. 171, 737-738.
2. Rippe K., Jovin T.M. 1992. Parallel-stranded duplex DNA. Methods Enzymol. 211 (Part A), 199-220.
3. Germann M.W., Zhou N., van de Sande J.H., Vogel H.J. 1995. Parallel-stranded duplex DNA: an NMR perspective. Methods Enzymol. 261, 207-226.
4. Shchyolkina A.K., Minchenkova L.E., Minyat E.E., Khomyakova Y.B., Ivanov V.I., Klement R., Jovin T.M. 1998. Distamycin-stabilized antiparallel-parallel combination (APC) DNA. J. Biomol. Struct. Dynam. 15, 823-839.
5. Cubero E., Avino A., de la Torre B.G., Frieden M., Eritja R., Luque F.J., Gonzalez C., Orosco M. 2002. Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives. J. Am. Chem. Soc. 124, 3133-3142.
6. Geinguenaud F., Liquier J., Brevnov M.G., Petrauskene O.V., Alexeev Y.I., Gromova E.S., Taillandier E. 2000. Parallel self-associated structures formed by T, C-rich sequences at acidic pH. Biochemistry. 39, 12650-12658.
7. Escude C., Mohammadi S., Sun J.-S., Nguen C-H., Bisagni E., Liquier J., Taillandier E., Garestier T., Helene C. 1996. Ligand-induced formation of Hoogsteen-paired parallel DNA. Chemistry and Biology. 3, 57-65.
8. Van de Sande J.H., Ramsing N.B., Germann M.W., Elhorst W., Kalisch B.W., von Kitzing E., Pon R.T., Clegg R.C., Jovin T.M. 1988. Parallel stranded DNA. Science. 241, 551-557.
9. Tchurikov N.A., Chernov B.K., Golova Yu.B., and Nechipurenko Yu.D. 1988. Parrallel-stranded DNA: possibility of existence. Dokl. Akad. Nauk SSSR. 303, 1254-1258.
10. Shchyolkina A.K., Lysov Y.P., Il'ichova I.A., Chernyi A.A., Golova Yu.B., Chernov B.K., Gottikh B.P., Florentiev V.L. 1989. Parallel stranded DNA with AT base pairing. FEBS Lett. 244, 39-42.
11. Tchurikov N.A., Nechipurenko Yu.D. 1991. Parallel complementary nucleotide sequences in natural DNA: hypothesis of parallel biosynthesis. Dokl. Akad. Nauk SSSR. 318, 1233-1238.
12. Kuryavyi V.V. 1987. Parallel DNA. Mol. Biol. 21, 1486-1496.
13. Rippe K., Kuryavyi V.V., Westhof E., Jovin T.M. 1992. in Structural Tools for the Analysis of Protein-Nucleic Acids Complexes. Eds Lilley D.M.J., Heumann M., Such D. Basel: Birkhauser Verlag, 81-107.
14. LeProust E.M., Pearson C.E., Sinden R.R., Gao X. 2000. Unexpected formation of parallel duplex in GAA and TTC trinucleotide repeats of Friedreich's Ataxia. J. Mol. Biol. 302, 1063-1080.
15. Suda T., Mishima Y., Asakura H., Kominami R. 1995. Formation of a parallel-stranded DNA homoduplex by d(GGA) repeat oligonucleotides. Nucleic Acids Res. 23, 3771-3777.
16. Robinson H., Wang A.H. 1993. 5′-CGA sequence is a strong motif for homo base-paired parallel-stranded DNA duplex as revealed by NMR analysis. Proc. Natl. Acad. Sci. USA. 90, 5224-5228.
17. Kejnovska I., Tumova M., Vorlickova M. 2001. (CGA)(4): parallel, anti-parallel, right-handed and left-handed homoduplexes of a trinucleotide repeat DNA. Biochim. Biophys. Acta. 1527, 73-80.
18. Otto C., Thomas G.A., Rippe K., Jovin T.M., Peticolas W.L. 1991. The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick. Biochemistry 30, 3062-3069.
19. Mohammadi S., Klement R., Shchyolkina A.K., Liquier J., Jovin T.M., Taillandier E. 1998. FTIR and UV spectroscopy of parallel-stranded DNAs with mixed A*T/G*C sequences and their A*T/I*C analogues. Biochemistry. 37, 16529-16537.
20. Rippe K., Ramsing N.B., Klement R., Jovin T.M. 1990. A parallel stranded linear DNA duplex incorporating dG.dC base pairs. J. Biomolec. Struct. Dynam. 7, 1199-1209.
21. Parvathy V.R., Bhaumik S.R., Chary K.V., Govil G., Liu K., Howard F.B., Miles H.T. 2002. NMR structure of a parallel-stranded DNA duplex at atomic resolution. Nucleic Acids Res. 30, 1500-1511.
22. Tchurikov N.A., Shchyolkina A.K., Borisova O.F., Chernov B.K. 1992. Southern molecular hybridization experiments with parallel complementary DNA probes. FEBS Lett. 297, 233-236.
23. Borisova O.F., Shchyolkina A.K., Chernov B.K., Tchurikov N.A. 1993. Relative stability of AT and GC pairs in parallel DNA duplex formed by a natural sequence. FEBS Lett. 322, 304-306.
24. Shchyolkina A.K., Borisova O.F., Livshits M.A., Pozmogova G.E., Chernov B.K, Jovin T.M. 2000. Parallel-stranded DNA with mixed AT/GC composition: role of trans GC base pairs in sequences dependent helical stability. Biochemistry. 39, 1039-1044.
25. Swaminathan V., Sundaralingam M. 1979. The crystal structures of metal complexes of nucleic acids and their constituents. CRC Crit. Rev. Biochem. 6, 245-336.
26. Seela F., Wei C., Melenewski A., Leonard P. 1997. Parallel-stranded duplexes and quartet assemblies formed by oligonucleotides containing isoguanine. Nucleic Acids Symp. Ser. 37, 149-150.
27. Sugiyama H., Ikeda S., Saito I. 1996. Remarkably stable parallel-stranded oligonucleotides containing 5-methyl-isocytosine and isoguanine. J. Am. Chem. Soc. 118, 9994-9995.
28. Yang X.L., Sugiyama H., Ikeda S., Saito I., Wang A.H. 1998. Structural studies of a stable parallel-stranded DNA duplex incorporating isoguanine:cytosine and isocytosine:guanine basepairs by nuclear magnetic resonance spectroscopy. Biophys J. 75, 1163-1171.
29. Shchyolkina A.K., Borisova O.F., Jovin T.M. 1999. Parallel-stranded oligonucleotides with alternating d(Ai-soG)/d(TC) and d(AG)/d(Tm5 isoG) sequences. Nucleosides & Nucleotides. 18, 1555-1562.
30. Rippe K., Jovin T.M. 1989. Substrate properties of 25-nt parallel-stranded linear DNA duplexes. Biochemistry. 28, 9542-9549.
31. Shchyolkina A.K., Borisova O.F., Livshits M.A., Klement R., Jovin T.M. 2001. The telomeric dG(GT)4G sequence can adopt a parallel-stranded double-helical conformation. J. Biomolecular Structure & Dynamics. 18, 493-503.
32. Kota R.S., Runge K.W. 1999. Tel2p, a regulator of yeast telomeric length in vivo, binds to single-stranded telomeric DNA in vitro. Chromosoma. 108, 278-290.
33. n repetitive sequences in solution. FEBS Lett. 306, 140-142.
34. Ramsing N.B., Rippe K., Jovin T.M. 1989. Helix-coil transition of parallel-stranded DNA. Thermodynamics of hairpin and linear duplex oligonucleotides. Biochemistry. 28, 9528-9535.
35. Germann M.W., Kalish B.W., Pon R.T., van de Sande J.H. 1990. Length-dependent formation of parallel-stranded DNA in alternating AT segments. Biochemistry. 29, 9426-9432.
36. n sequences: formation of parallel stranded duplex DNA. Biochemistry. 37, 12962-12970.
37. Fritzsche H., Akhebat A., Taillandier E., Rippe K., Jovin T.M. 1993. Structure and drug interactions of parallel-stranded DNA studied by infrared spectroscopy and fluorescence. Nucleic Acids Res. 21, 5085-5091.
38. Rippe K., Fritsch V., Westhof E., Jovin T.M. 1992. Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex. EMBO J. 11, 3777-3786.
39. Shchyolkina A.K., Kaluzhny D.N., Borisova O.F., Hanley Q., Layton A., Jovin D.J., Jovin T.M. 2001. 2-aminopurine as a probe for parallel or antiparallel orientaion of strands in DNA duplex. J. Biomol. Struct. & Dynamics. 18, 941-942.