STRUCTURAL TRANSITIONS IN POLYCYTIDYLIC ACID: PROTON BUFFER CAPACITY DATA

References

• Chen , Z. , Li , Y. and Krug , R.M. 1999 . Influenza A virus NSI Protein Targets polyA-Binding Protein II of the Cellular 3′-end Processing Machinery . EMBO J. , 18 ( 8 ) : 2273 – 2283 .
   PubMedGoogle Scholar
• Wang , Z. , Day , N. , Trifillis , P. and Kiledjian , M. 1999 . An mRNA Stability Complex Functions with Poly(A)-Binding Protein to Stabilize mRNA in vitro . Mo. Cell. Biol. , 19 ( 7 ) : 4552 – 4560 .
   Google Scholar
• Decker , C.J. and Parker , R.A . 1993 . Turnover Pathway for Both Stable and Unstable mRNAs in Yeast: Evidence for a Requirement for Deadenylation . Genes & Dev. , 7 ( 8 ) : 1632 – 1643 .
   PubMed Web of Science ®Google Scholar
• Sachs , A.B. , Sarnow , P. and Hentze , M.W. 1997 . Starting at the Beginning, Middle and End: Translation Initiation in Eukaryotes. . Cell , 89 ( 6 ) : 831 – 838 .
   PubMedGoogle Scholar
• Zarudnaya , M.I. and Hovorun , D.M. 1999 . Hypothetical Double-Helical Poly(A) Formation in a Cell and Its Possible Biological Significance . IUBMB Life , 48 ( 6 ) : 581 – 584 .
   PubMedGoogle Scholar
• Zimmerman , S.B. , Cohen , G.H. and Davies , D.R. 1975 . X-ray Fiber Diffraction and Model-building Study of Polyguanylic Acid and Polyinosinic Acid . J. Mol. Biol. , 92 ( 2 ) : 181 – 192 .
   PubMedGoogle Scholar
• Williamson , J.R. , Raghuraman , M.K. and Cech , T.R. 1989 . Monovalent Cation-Inducèd Structure of Telomeric DNA: the G-quartet Model . Cell , 59 ( 5 ) : 871 – 880 .
   PubMed Web of Science ®Google Scholar
• Muniyappa , K. , Anuradha , S. and Byers , B. 2000 . Yeast Meiosis-Specific Protein Hop 1 binds to G4 DNA and Promotes its Formation . Mol. Cell. Biol. , 20 ( 4 ) : 1361 – 1369 .
   PubMedGoogle Scholar
• Dempsey , L.A. , Sun , H. , Hanakahi , L.A. and Maizels , N. 1999 . G4 DNA Binding By LRI and its Subunits, Nucleolin and hnRNP D, a role for G-G Pairing in Immunoglobubin Switch Recombination . J. Biol. Chem. , 274 ( 2 ) : 1066 – 1071 .
   PubMedGoogle Scholar
• Simon , R. and Richter , J.D. 1994 . Further Analysis of Cytoplasmic Polyadenylation in Xenopus Embryos and Identification of Embryonic Cytoplasmic Poly-adenylation Element-Binding Proteins . Mol. Cell. Biol. , 14 ( 12 ) : 7867 – 7875 .
   PubMedGoogle Scholar
• Paillard , L. , Maniey , D. , Lachaume , P. , Legagneux , V. and Osborne , H.B. 2000 . Identification of a C-rich Element as a Novel Cytoplasmic Polyadenylation Element in Xenopus Embryos . Mech. Dev. , 93 ( 1–2 ) : 117 – 125 .
   PubMedGoogle Scholar
• Black , D.N. , Stephenson , P. , Rowlands , D.J. and Brown , F. 1979 . Sequence and Location of the Poly C Tract in Aphtho- and Cardiovirus RNA . Nucleic Acids Res. , 6 ( 7 ) : 2381 – 2390 .
   PubMedGoogle Scholar
• Martin , L.R. , Neal , Z.C. , McBride , M.S. and Palmenberg , A.C. 2000 . Mengovirus and encephalomyocarditis Virus Poly(C) Tract Lengths Affect Virus Growth in Murine Cell Culture . J. Virol. , 74 ( 7 ) : 3074 – 3081 .
   PubMedGoogle Scholar
• Michelson , A.M. , Massoulié , J. and Guschlbauer , W. 1967 . “ Synthetic Polynucleotides ” . In Progress In Nucleic Acid Research and Molecular Biology Vol. 6 , 83 – 141 . New York, London : Academic Press .
   Google Scholar
• Samijlenko , S.P. , Kolomiets , I.M. , Kondratyuk , I.V. and Stepanyugin , A.V. 1998 . Model Considerations on Physico-Chemical Nature of Protein-Nucleic acid Contacts Through Amino Acid Carboxylic Groups: Spectroscopic Data . Biopolimery i kletka , 14 ( 1 ) : 47 – 53 .
   Google Scholar
• Hartman , K.A. , McDonald-Ordzie , P.E. , Kaper , J.M. , Prescott , B. and Thomas , G.J. Jr. 1978 . Studies of Virus Structure by Laser-Raman Spectroscopy. Turnip Yellow Mosaic Virus and Capsids . Biochemistry , 17 ( 11 ) : 2118 – 2123 .
   PubMedGoogle Scholar
• Prescott , B. , Sitaraman , K. , Argos , P. and Thomas , G.J. Jr. 1985 . Protein–RNA interactions in Belladonna Mottle Virus Investigated by Laser Raman Spectroscopy . Biochemistry , 24 ( 5 ) : 1226 – 1231 .
   PubMedGoogle Scholar
• Hellendoorn , K. , Michiels , P.J.A. , Buitenhuis , R. and Pleij , C.W.A. 1996 . Protonatable Hairpins are Conserved in the 5′-Untranslated Region of Tymovirus RNAs . Nucleic Acids Res. , 24 ( 24 ) : 4910 – 4917 .
   PubMedGoogle Scholar
• Broido , M.S. and Kearns , D.R. 1982 . 1H NMR Evidence for a Left-Handed Helical Structure of Poly(ribocytidylic acid) in Neutral Solution . J. Am. Chem. Soc. , 104 ( 19 ) : 5207 – 5216 .
   Google Scholar
• Guschlbauer , W. 1975 . Protonated Polynucleotide Structures. 16. Thermodynamics of the Melting of the Acid Form of Polycytidylic Acid . Nucleic Acids Res. , 2 ( 3 ) : 353 – 360 .
   PubMedGoogle Scholar
• Akinrimisi , E.O. , Sander , C. and Ts'o , P.O.P. 1963 . Properties of Helical Polycytidylic acid . Biochemistry , 2 ( 2 ) : 340 – 344 .
   PubMedGoogle Scholar
• Hartman , K.A. and Rich , A. 1965 . The Tautomeric Form of Helical Polyribocytidylic Acid . J. Am. Chem. Soc. , 87 ( 9 ) : 2033 – 2039 .
   PubMedGoogle Scholar
• Guschlbauer , W. 1967 . Protonated Polynucleotide Structures. I. The Thermal Denaturation of Polycytidylic Acid in Acid Solution . Proc. Natl. Acad. Sci. USA , 57 ( 5 ) : 1441 – 1448 .
   PubMedGoogle Scholar
• Klump , H. 1975 . A Calorimetric Study of the Helix-coil Transition of Poly(cytidylic acid) in Acid Solution . Biochim. Biophys. Acta. , 383 ( 1 ) : 1 – 8 .
   PubMedGoogle Scholar
• Antao , V.P. and Gray , D.M. 1993 . CD Spectral Comparisons of the Acid-Induced Structures of Poly[dA] Poly[r(A)], Poly[dC] and Poly[rC] . J. Biomol. Struct. Dyn. , 10 ( 5 ) : 819 – 839 .
   PubMed Web of Science ®Google Scholar
• Chou , C.H. and Thomas , G.J. Jr. 1977 . Raman Spectral Studies of Nucleic acids. XVI. Structures of Polyribocytidylic acid in Aqueous Solution . Biopolymers , 16 ( 4 ) : 765 – 789 .
   PubMedGoogle Scholar
• Langridge , R. and Rich , A. 1963 . Molecular Structure of Helical Polycytidylic acid . Nature , 198 ( 4882 ) : 725 – 728 .
   PubMedGoogle Scholar
• Suleimanova , R.S. , Apolonnik , N.V. and Kuznetsov , I.A. 1987 . Acid-Basic Properties of Isoionic Solutions of Polyribocytidylic acid . Biofizika (Russian) , 32 ( 3 ) : 413 – 416 .
   Google Scholar
• Apolonnik , N.V. , Suleimanova , R.S. and Kuznetsov , I.A. 1987 . Conductometric Support for Existence of Completely Protonated Double helix of Polyribocytidylic acid . Mol. Biol. , 21 ( 2 Part 2 ) : 361 – 365 .
   Google Scholar
• Opanasenko , V.K. , Gerts , S.M. and Makarov , A.D. 1978 . Buffer Capacity of Polyproton Objects . Biochemistry (U.S.S.R.) , 43 ( 8 Part 1 ) : 1068 – 1075 .
   Google Scholar
• Sukhorukov , B.I. , Montrel' , M.M. , Opanasenko , V.K. and Zolotareva , E.K. 1983 . The Interaction of DNA with Protons of the Medium by the Buffer Capacity Method . Mol. Biol. , 17 ( 5 Part 2 ) : 822 – 829 .
   Google Scholar
• Zarudnaya , M.I. 1998 . Study of Conformational Transitions in Poly(A) by the Buffer Capacity Technique . Mol. Biol. , 32 ( 3 ) : 417 – 422 .
   Google Scholar
• Guschlbauer , W. , Blandin , M. , Drocourt , J.L. and Thang , M.N. 1977 . Poly-2′-deoxy-2′-fluoro-cytidylic Acid: Enzymatic Synthesis, Spectroscopic Characterization and Interaction with Poly-Inosinic Acid . Nucleic Acids Res. , 4 ( 6 ) : 1933 – 1943 .
   PubMedGoogle Scholar
• Thiele , D. and Guschlbauer , W. 1969 . Protonated Polynucleotides. VII. Thermal Transitions Between Different Complexes of Polyinosinic acid and Polycytidylic acid in an Acid Medium . Biopolymers , 8 ( 3 ) : 361 – 378 .
   PubMedGoogle Scholar
• Aronssohn , G. and Travers , F. 1976 . Electrostatic Potential Modulations on Polynucleotides as a Function of Ionic Content: Potentiometric Determinations . Nucleic Acids Res. , 3 ( 5 ) : 1373 – 1385 .
   PubMedGoogle Scholar
• S˘poner , J. , Leszczyński , J. and Hobza , P. 1996 . Hydrogen Bonding and Stacking of DNA Bases: a Review of Quantum-Chemical ab initio Studies . J. Biomol. Struct. Dyn. , 14 ( 1 ) : 117 – 135 .
   PubMed Web of Science ®Google Scholar
• Hovorun , D.M. and Kondratyuk , I.V. 1998 . The Gas-Phase Acidic-Basic Properties of Canonical Nucleotide Bases . Dopovidi NAN Ukrainy (Ukrainian) , 1 : 207 – 212 .
   Google Scholar
• Florian , J. , Baumruk , V. and Leszczynski , J. 1996 . IR and Raman Spectra, Tautomeric Stabilities, and Scaled Quantum Mechanical Force Fields of Protonated Cytosine . J. Phys. Chem. , 100 ( 13 ) : 5578 – 5589 .
   Google Scholar
• Voityuk , A.A. and Bliznyuk , A.A. 1988 . Influence of Protonation of Nucleic Bases Upon Energy of Formation of Watson-Crick Pairs . Mol. Biol. , 22 ( 4 Part 2 ) : 870 – 875 .
   Google Scholar
• Mishchuk , Ya.R. and D.M. 1998 . Intramolecular Hydrogen Bonds and Structural Nonrigidity of Pyrimidine Nucleosides . Biopolimery i Kletka , 14 ( 4 ) : 360 – 370 .
   Google Scholar
• Sowers , L.C. , Shaw , B.R. , Veigl , M.L. and Sedwick , W.D. 1987 . DNA Base Modification: Ionized Base Pairs and Mutagenesis . Mutation Res. , 177 ( 2 ) : 201 – 218 .
   PubMedGoogle Scholar
• Wróbel , A. , Rabczenko , A. and Shugar , D. 1970 . Conformation of Acid Forms of polyC: Temperature and Ionic Strength Dependence of Protonation of Cytidine and Cytidine-5′-phosphate . Acta Biochim. Polonica , 17 ( 4 ) : 339 – 349 .
   PubMedGoogle Scholar
• Green , G. and Mahler , H.R. 1970 . Comparative Study of Polyribonucleotides in Aqueous and Glycol solutions . Biochemistry , 9 ( 2 ) : 368 – 387 .
   PubMedGoogle Scholar
• O'Connor , T. and Scovell , W.M. 1981 . pH-Dependent Raman Spectra and Thermal Melting Profiles for Polycytidylic acid . Biopolymers , 20 ( 11 ) : 2351 – 2367 .
   Google Scholar
• Gehring , K. , Leroy , J.-L. and Guéron , M. 1993 . A Tetrameric DNA Structure with Protonated Cytosine·Cytosine Base Pairs . Nature , 363 ( 6429 ) : 561 – 565 .
   PubMed Web of Science ®Google Scholar
• Guéron , M. and Leroy , J.-L. 2000 . The i-motif in Nucleic acids . Curr. Opin. Struct. Biol. , 10 ( 3 ) : 326 – 331 .
   PubMedGoogle Scholar
• Lacroix , L. , Mergny , J.-L. , Leroy , J.-L.; and Héléne , C. 1996 . Inability of RNA to Form the i-motif: Implications for Triplex Formation . Biochemistry , 35 ( 26 ) : 8715 – 8722 .
   PubMedGoogle Scholar
• Collin , D. and Gehring , K. 1998 . Stability of Chimeric DNA/RNA Cytosine Tetrads: Implications for i-motif Formation by RNA . J. Am. Chem. Soc. , 120 ( 17 ) : 4069 – 4072 .
   Google Scholar
• Snoussi , K. , Nonin-Lecomte , S. and J.-L. 2001 . The RNA i-motif . J. Mol. Biol. , 309 ( 1 ) : 139 – 153 .
   PubMedGoogle Scholar
• Opanasenko , V.K. 1980 . A Technique for Assaying Chloroplast Buffer Capacity and Analysis of Its Dependence on the Medium pH . Fiziologiya Rastenii Russian , 27 ( 1 ) : 195 – 202 .
   Google Scholar