Synthesis and Evaluation of Oligonucleotide-Conjugated Pyrrole Polyamide-2′-Deoxyguanosine Hybrids as Novel Gene Expression Control Compounds

REFERENCES

• Cook , P. D. 2000 . “ A brief history, status, and perspective of modified oligonucleotides for chemotherapeutic applications ” . In Current Protocols in Nucleic Acid Chemistry , Edited by: Beaucage , S. L. , Bergstrom , D. E. , Glick , G. D. and Jones , R. A. Vol. 4 , 4.1.1 – 4.1.17 . New York : John Wiley & Sons .
   Google Scholar
• Pelton , J. G. and Wemmer , D. E. 1989 . Structural characterization of a 2:1 distamycin A-d(CGCAAATTGGC) complex by two-dimensional NMR . Proc. Natl. Acad. Sci. USA , 86 : 5723 – 5727 .
   PubMed Web of Science ®Google Scholar
• Baird , E. E. and Dervan , P. B. 1996 . Solid phase synthesis of polyamides containing imidazole and pyrrole amino acids . J. Am. Chem. Soc. , 118 : 6141 – 6146 .
   Web of Science ®Google Scholar
• Boger , D. L. , Fink , B. E. and Hedrick , M. P. 2000 . Total synthesis of distamycin and 2640 analogues: a solution-phase combinatorial approach to the discovery of new, bioactive DNA binding agents and development of a rapid, high-throughput screen for determining relative DNA binding affinity or DNA binding sequence selectivity . J. Am. Chem. Soc. , 122 : 6382 – 6394 .
   Web of Science ®Google Scholar
• Kawashima , E. , Itoh , D. , Kamaike , K. , Terui , Y. and Oshima , T. 2003 . Synthesis and analysis of nucleosides bearing pyrrolepolyamide binding to DNA . Nucleosides Nucleotides Nucleic Acids , 22 : 1309 – 1311 .
   PubMed Web of Science ®Google Scholar
• Ohba , Y. , Kamaike , K. , Terui , Y. , Oshima , T. and Kawashima , E. 2003 . Design, synthesis and analysis of antiviral nucleosodes bearing pyrrole polyamide binding to nucleic acid (II): N 2-pyrrolepolyamidopropylguanosine . Nucleic Acids Res. Suppl. , 3 : 29 – 30 .
   PubMedGoogle Scholar
• Ohba , Y. , Terui , Y. , Kamaike , K. , Oshima , T. and Kawashima , E. 2004 . Design, synthesis and analysis of a pyrrole polyamide-nucleoside hybrid . Nucleic Acids Res. Suppl. , 48 : 55 – 56 .
   Google Scholar
• Kawashima , E. , Ohba , Y. , Terui , Y. and Kamaike , K. 2010 . Design, synthesis, and analysis of minor groove binder pyrrole polyamide-2′-deoxyguanosine hybrid . J. Nucleic Acids , Article ID 235240 : 13 pp
   Google Scholar
• Rentzeperis , D. , Marky , L. A. , Dwyer , T. J. , Geierstanger , B. H. , Pelton , J. G. and Wemmer , D. E. 1995 . Interaction of minor groove ligands to an AAATT/AATTT site: correlation of thermodynamic characterization and solution structure . Biochemistry , 34 : 2937 – 2945 .
   PubMed Web of Science ®Google Scholar
• Lah , J. and Vesnaver , G. 2000 . Binding of distamycin A and netropsin to the 12mer DNA duplexes containing mixed AT-GC sequences with at most five or three successive AT base pairs . Biochemistry , 39 : 9317 – 9326 .
   PubMed Web of Science ®Google Scholar
• Levina , A. S. , Metelev , V. G. , Cohen , A. S. and Zamecnik , P. C. 1996 . Conjugates of minor groove DNA binder with oligodeoxynucleotides: synthesis and properties . Antisense Nucleic Acid Drug Dev. , 6 : 75 – 85 .
   PubMedGoogle Scholar
• Szewczyk , J. W. , Baird , E. E. and Dervan , P. B. 1996 . Sequence-specific recognition of DNA by a major and minor groove binding ligand . Angew. Chem. Ind. Ed. Engl. , 35 : 1487 – 1489 .
   Web of Science ®Google Scholar
• Novopashina , D. , Sinyakov , A. , Ryabinin , V. , Venyaminova , A. and Boutorine , A. 2003 . Conjugates of oligo(2′-O-methylribonucleotides) with minor groove binders as new sequence-specific agents recognizing both grooves of double-stranded DNA . Nucleosides Nucleotides Nucleic Acids , 22 : 1179 – 1182 .
   PubMed Web of Science ®Google Scholar
• Boutorine , A. S. , Ryabinin , V. A. , Novopashina , D. S. , Venyaminova , A. G. , Helene , C. and Sinyakov , A. S. 2003 . Stabilization of DNA double and triple helices by conjugation of minor groove binders to oligonucleotides . Nucleosides Nucleotides Nucleic Acids , 22 : 1267 – 1272 .
   PubMed Web of Science ®Google Scholar
• Ryabinin , V. A. , Boutorine , A. S. , Helene , C. , Pyshnyi , D. V. and Sinyakov , A. N. 2004 . Oligonucleotide-minor groove binder conjugates and their complexes with complementary DNA: effect of conjugate structural factors on the thermal stability of duplexes . Nucleosides Nucleotides Nucleic Acids , 23 : 789 – 803 .
   PubMed Web of Science ®Google Scholar
• Ryabinin , V. A. , Boutorine , A. S. , Helene , C. , Denisov , A. Y. , Pyshnyi , D. V. and Sinyakov , A. N. 2004 . Oligonucleotide-minor groove binder 1:2 conjugates: side by side parallel minor groove binder motif in stabilization of DNA duplex . Nucleosides Nucleotides Nucleic Acids , 23 : 953 – 968 .
   PubMed Web of Science ®Google Scholar
• Novopashina , D. S. , Sinyakov , A. N. , Ryabinin , V. A. , Venyaminova , A. G. , Perrouault , L. , Brunet , E. , Giovannangeli , C. and Boutorine , A. S. 2004 . Binding properties of conjugates of oligo(2′-O-methylribonucleotides) with minor groove binders targeted to double stranded DNA . Nucleosides Nucleotides Nucleic Acids , 23 : 1015 – 1022 .
   PubMed Web of Science ®Google Scholar
• Novopashina , D. S. , Sinyakov , A. N. , Ryabinin , V. A. , Venyaminova , A. G. , Halby , L. , Sun , J.-S. and Boutorine , A. S. 2005 . Sequence-specific conjugates of oligo(2′-O-methylribonucleosides) and hairpin oligogarboxamide minor-groove binder: design, synthesis, and binding studies with double-stranded DNA . Chem. Biodiversity , 2 : 936 – 952 .
   PubMed Web of Science ®Google Scholar
• Sung , W. L. 1981 . Synthesis of 4-triazolopyrimidinone nucleotide and its application in synthesis of 5-methylcytosine containing oligodeoxyribonucleotides . Nucleic Acids Res. , 9 : 6139 – 6151 .
   PubMed Web of Science ®Google Scholar
• Webb , T. R. and Matteucci , M. D. 1986 . Hybridization triggered cross-linking of deoxyoligonudeotides . Nucleic Acids Res. , 14 : 7611 – 7674 .
   Web of Science ®Google Scholar
• Cowart , M. , Gibson , K. J. , Allen , D. J. and Benkovic , S. J. 1989 . DNA substrate structural requirements for the exonuclease and polymerase activities of prokaryotic and phage DNA polymerases . Biochemistry , 28 : 1975 – 1983 .
   PubMed Web of Science ®Google Scholar
• MacMillan , A. M. and Verdine , G. L. 1990 . Synthesis of functionally tethered oligodeoxynucleotides by the convertible nucleoside approach . J. Org. Chem. , 55 : 5931 – 5933 .
   Web of Science ®Google Scholar
• Fernandez-Forner , D. , Palom , Y. , Ikuta , S. , Pedroso , E. and Eritja , R. 1990 . Synthesis and characterization of oligodeoxynucleotides containing the mutagenic base analogue 4-O-ethylthymine . Nucleic Acids Res. , 18 : 5729 – 5734 .
   PubMed Web of Science ®Google Scholar
• Xu , Y.-Z. , Zheng , Q. and Swann , P. F. 1992 . Synthesis of DNA containing modified bases by postsynthetic substitution. Synthesis of oligomers containing 4-substituted thymine: O 4-alkylthymine, 5-methylcytosine, N 4-(dimethylamino)-5-methylcytosine, and 4-thiothymine . J. Org. Chem. , 57 : 3839 – 3845 .
   Web of Science ®Google Scholar
• Gao , H. , Fathi , R. , Gaffney , B. L. , Goswami , B. , Kung , P.-P. , Rhee , Y. , Jin , R. and Jones , A. 1992 . 6-O-(pentafluorophenyl)-2′-deoxyguanosine: a versatile synthon for nucleoside and oligonucleotide synthesis . J. Org. Chem. , 57 : 6954 – 6959 .
   Web of Science ®Google Scholar
• Xu , Y.-Z. , Zheng , Q. and Awann , P. F. 1992 . Synthesis by post-synthetic substitution of oligomers containing guanine modified at the 6-position with S-, N-, O-derivatives . Tetrahedron , 48 : 1729 – 1740 .
   Web of Science ®Google Scholar
• Kim , S. J. , Stone , M. P. , Harris , C. M. and Harris , T. M. 1992 . A postoligomerization synthesis of oligodeoxynucleotides containing polycyclic aromatic hydrocarbon adducts at the N 6 position of deoxyadenosine . J. Am. Chem. Soc. , 114 : 5480 – 5481 .
   Web of Science ®Google Scholar
• Ono , A. , Haginoya , N. , Kiyokawa , M. , Minakawa , M. and Matsuda , A. 1994 . Nucleosides and nucleotides. 127. A novel and convenient post-synthetic modification method for the synthesis of oligodeoxyribonucleotides carrying amino linker at the 5 position of 2′-deoxyuridine . Bioorg. Med. Chem. Lett. , 4 : 361 – 366 .
   Web of Science ®Google Scholar
• Harris , C. M. , Zhou , L. , Strand , E. A. and Harais , T. M. 1991 . New strategy for the synthesis of oligonucleotides bearing adducts at exocyclic amino site of purine nucleosides . J. Am. Chem. Soc. , 113 : 4328 – 4329 .
   Web of Science ®Google Scholar
• Schmid , N. and Behr , J.-P. 1995 . Recognition of DNA sequences by strand replacement with polyamino-oligonucleotides . Tetrahedron Lett. , 36 : 1447 – 1450 .
   Web of Science ®Google Scholar
• Adib , A. , Potier , P. F. , Doronina , S. , Huc , I. and Behr , J.-P. 1997 . A high-yield synthesis of deoxy-2-fluoroinosine and its incorporation into oligonucleotides . Tetrahedron Lett. , 38 : 2989 – 2992 .
   Web of Science ®Google Scholar
• Shinozuka , K. , Onodera , M. , Ikeda , H. and Sawai , H. 2002 . Duplex stabilizing effect and nuclease resistant property of novel oligonucleotides containing C-2 branched polyamine-bearing deoxyinosine derivative . Chem. Lett. , 2 : 200 – 201 .
   Google Scholar
• Lee , H. , Hinz , M. , Stezowski , J. J. and Harvey , R. G. 1990 . Syntheses of polycyclic aromatic hydrocarbon-nucleoside and oligonucleotides adducts specifically alkylated on the amino functions of deoxyguanosine and deoxyadenosine . Tetrahedron Lett , 31 : 6773 – 6776 .
   Web of Science ®Google Scholar
• Wade , W. S. , Mrksich , M. and Dervan , P. B. 1992 . Design of peptides that bind in the minor groove of DNA at 5′-(A,T)G(A,T)C(A,T)-3′ sequences by a dimeric side-by-side motif . J. Am. Chem. Soc. , 114 : 8783 – 8794 .
   Web of Science ®Google Scholar
• White , S. , Baird , E. E. and Dervan , P. B. 1997 . Orientation preferences of pyrrole-imidazole polyamides in the minor groove of DNA . J. Am. Chem. Soc. , 119 : 8756 – 8765 .
   Web of Science ®Google Scholar
• Dervan , P. D. 2001 . Molecular recognition of DNA by small molecules . Bioorg. Med. Chem. , 9 : 2215 – 2235 .
   PubMed Web of Science ®Google Scholar
• Kamaike , K. , Kinoshita , K. , Niwa , K. , Hirose , K. , Suzuki , K. and Ishido , Y. 2001 . Efficient methods for the synthesis of [2–15N]guanosine and 2′-deoxy[2–15N]guanosine derivatives . Nucleosides Nucleotides Nucleic Acids , 20 : 59 – 75 .
   PubMed Web of Science ®Google Scholar
• Sinha , N. D. , Biernat , J. , McManus , J. and Köster , H. 1984 . Polymer support oligonucleotide synthesis XVIII: use of β-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product . Nucleic Acids Res. , 12 : 4539 – 4557 .
   PubMed Web of Science ®Google Scholar
• “ Synthesis of modified oligonucleotides [5′-d(CGMAATTTGGC)-3′ (MALDI-TOFMS calcd. for C135H167N50O69P10 (M+H)+ 3901.85, found 3903.77), 5′-d(CGMACTTTGGC)-3′ (MALDI-TOFMS calcd. for C134H167N48O70P10 (M+H)+ 3877.84, found 3880.11), 5′-d(CGMAATCTGGC)-3′ (MALDI-TOFMS calcd. for C134H166N51O68P10 (M+H)+ 3886.85, found 3883.09), and 5′-d(CGMAGTCTGGC)-3′ (MALDI-TOFMS calcd. for C134H166N50O69P10 (M+H)+ 3902.84, found 3900.90): M = Hybrid 2] using phosphoramidite 18 was performed by Hokkaido System Science Co., Ltd. Mass spectra were recorded on a Applied Biosystems Voyager System 2073 ” .
   Google Scholar
• Gait , M. J. , Matthes , H. W.D. , Singh , M. , Sproat , B. S. and Titmas , R. 1982 . Continuous-flow phosphotriester method for solid-phase synthesis of oligodeoxyribonucleotides . Cold Spring Harbor Symp. Quant. Biol. , 47 : 393 – 401 .
   Google Scholar
• Kopka , X. L. , Yoon , C. , Goodsell , D. , Pjura , P. and Dickerson , R. E. 1985 . The molecular origin of DNA-drug specificity in netropsin and distamycin . Proc. Natl. Acad. Sci. USA , 82 : 1376 – 1380 .
   PubMed Web of Science ®Google Scholar
• Lown , J. W. , Krowicki , K. , Bhat , U. G. , Skorobogaty , A. , Ward , B. and Dabrowiak , J. C. 1986 . Molecular recognition between oligonucleotides and nucleic acids: novel imidazole-containing oligopeptides related to netropsin that exhibit altered DNA sequence specificity . Biochemistry , 25 : 7408 – 7416 .
   PubMed Web of Science ®Google Scholar
• White , S. , Baird , E. E. and Dervan , P. B. 1997 . Orientation preferences of pyrrole-imidazole polyamides in the minor groove of DNA . Chem. Biol. , 4 : 569 – 578 .
   PubMedGoogle Scholar
• Marky , L. A. and Breslauer , K. J. 1987 . Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves . Biopolymers , 26 : 1601 – 1620 .
   PubMed Web of Science ®Google Scholar