Complex Formation between Polycytidylic Acid and Guanine Oligonucleotides

Lipsett, Marie N.

doi:10.1016/s0021-9258(18)91420-1

Cited by 125 publications

(15 citation statements)

References 12 publications

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“…Base Triple Combinations, Pairing Alignments, and Strand Orientation. Analogous to U-AU and C+-GC combinations in ribonucleotides (Felsenfeld et al, 1957;Lipsett, 1964), T-AT and C+-GC combinations indeoxyribonucleotides (Riley et al, 1966;Lee et al, 1979) were identified by early studies on triplex polymers. Recent studies have revealed at least two additional base triple combinations within this motif, including G-TA (Griffin & Dervan, 1989) and T-CG (Yoon et al, 1992).…”

Section: Y-ry Triplexesmentioning

confidence: 99%

“…Base Triple Combinations, Pairing Alignments, and Strand Orientation. Early studies exploring possible base triple combinations in this motif utilized optical spectroscopy and ultracentrifugation measurements which led to the identification of G*GC and HC base triple combinations (Lipsett, 1964; Inman, 1964; Marck & Thiele, 1978). More recently, however, Fresco and co-workers scanned the full spectrum of base triple combinations using affinity chromatography and identified additional interactions including A-AU/T, FAU/ T, and I-GC triples in homopolymers (Letai et al, 1988).…”

Section: R'ry Triplexesmentioning

confidence: 99%

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DNA Triplexes: Solution Structures, Hydration Sites, Energetics, Interactions, and Function

Radhakrishnan¹,

Patel²

1994

Biochemistry

232

172

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Historical Perspective. The formation of a specific complex between two strands of poly(uridylic acid) with one strand of poly(adenylic acid) in the presence of divalent cations was first described by Felsenfeld et al. (1957). Subsequently, triple-stranded complexes containing other combinations of polynucleotide strands were described including those belonging to the deoxyribose series [reviewed in Felsenfeld and Miles (1967), Wells et al. (1988), Cheng and Pettitt (1992b), and Sun and H61Sne (1993)]. These studies culminated in lowresolution, X-ray fiber-diffraction models for the (A)"-2(U)", (A)"'2(I)", and (A)"-2(T)" combinations (Arnott & Seising, 1974, and references cited therein). Further, a potential biological function for these structures was identified when they were found to inhibit RNA1 polymerase-mediated transcription in vitro (Morgan & Wells, 1968).Interest in triplexes revived following the discovery of singlestrand-specific SI endonuclease hypersensitive sites in the upstream regions of several eukaryotic genes (Larsen & Weintraub, 1982). These sites were mapped to (R)"-(Y)" sequences which, when subcloned into supercoiled plasmids, exhibited the same sensitivity toward SI nuclease [reviewed + This work was supported under NIH Grant GM 34504 to D.J.P.A Coordinates for the Y-RY triplexes containing G*TA (Accession No. 149D) and T-CG (Accession No. 177D) triples and the R-RY triplex (Accession Nos. 134D, 135D, 136D) have been deposited with the Protein Data Bank, Brookhaven National Laboratory, Upton, NY 11973, from whom copies can be obtained.

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Section: Y-ry Triplexesmentioning

confidence: 99%

Section: R'ry Triplexesmentioning

confidence: 99%

DNA Triplexes: Solution Structures, Hydration Sites, Energetics, Interactions, and Function

Radhakrishnan¹,

Patel²

1994

Biochemistry

232

172

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“…The G * C base pair was originally shown to be bound by third strand C or G residues in studies with polyribonucleotides (4,5). In those studies it was shown that the interaction of C with G * C base pairs is at best weak at neutrality, being considerably stabilized as the pH is decreased.…”

Section: Introductionmentioning

confidence: 99%

UV spectroscopic identification and thermodynamic analysis of protonated third strand deoxycytidine residues at neutrality in the triplex d(C⁺-T)6:[d(A-G)6d(C⁻-T)6]; evidence for a proton switch

Lavelle¹,

Fresco²

1995

Nucl Acids Res

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Near-UV difference spectral analysis of the triplex formed from d(C-T)6 and d(A-G)6.d(C-T)6 in neutral and acidic solution shows that the third strand dC residues are protonated at pH 7.0, far above their intrinsic pKa. Additional support for ion-dipole interactions between the third strand dC residues and the G.C target base pairs comes from reduced positive dependence of triplet stability on ionic strength below 0.9 M Na+, inverse dependence above 0.9 M Na+ and strong positive dependence on hydrogen ion concentration. Molecular modeling (AMBER) of C:G.C and C+:G.C base triplets with the third strand base bound in the Hoogsteen geometry shows that only the C+:G.C triplet is energetically feasible. van't Hoff analysis of the melting of the triplex and target duplex shows that between pH 5.0 and 8.5 in 0.15 M NaCl/0.005 M MgCl2 the enthalpy of melting (delta H degree obs) varies from 5.7 to 6.6 kcal.mol-1 for the duplex in a duplex mixture and from 7.3 to 9.7 kcal.mol-1 for third strand dissociation in the triplex mixture. We have extended the condensation-screening theory of Manning to pH-dependent third strand binding. In this development we explicitly include the H+ contribution to the electrostatic free energy and obtain [formula: see text]. The number of protons released in the dissociation of the third strand from the target duplex at pH 7.0, delta n2, is thereby calculated to be 5.5, in good agreement with approximately six third strand dc residues per mole of triplex. This work shows that when third strand binding requires protonated residues that would otherwise be neutral, triplex formation and dissociation are mediated by proton uptake and release, i.e., a proton switch. As a by-product of this study, we have found that at low pH the Watson-Crick duplex d(A-G)6.d(C-T)6 undergoes a transition to a parallel Hoogsteen duplex d(A-G)6.d(C(+)-T)6.

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“…35,36 Since then, a number of triplex DNA structures that form under various conditions in vitro and/or in vivo have been identified. [37][38][39][40][41] In 1987, short oligonucleotides (triplex-forming oligonucleotides (TFO)) were also found to be able to bind in the major groove of the DNA duplex to form the triple-helical structures (Fig. 4).…”

Section: Structure and Biological Function Of Triplex Dnamentioning

confidence: 99%

Recognition and regulation of unique nucleic acid structures by small molecules

Song

Ren

2010

Chem. Commun.

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DNA and RNA are both polymorphic. Depending on the sequences and environmental conditions, they could exist in a variety of secondary structures that play key roles in many biological processes. Recognition of these structures by small ligands is very important for the development of new drugs and new tools. In this article, we will focus on recent advances in the field of molecular recognition and regulation of small ligands with several unique nucleic acid structures, and we will also highlight some of their potential applications in medicinal chemistry and biotechnology.

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Complex Formation between Polycytidylic Acid and Guanine Oligonucleotides

Cited by 125 publications

References 12 publications

DNA Triplexes: Solution Structures, Hydration Sites, Energetics, Interactions, and Function

DNA Triplexes: Solution Structures, Hydration Sites, Energetics, Interactions, and Function

UV spectroscopic identification and thermodynamic analysis of protonated third strand deoxycytidine residues at neutrality in the triplex d(C⁺-T)6:[d(A-G)6d(C⁻-T)6]; evidence for a proton switch

Recognition and regulation of unique nucleic acid structures by small molecules

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Complex Formation between Polycytidylic Acid and Guanine Oligonucleotides

Cited by 125 publications

References 12 publications

DNA Triplexes: Solution Structures, Hydration Sites, Energetics, Interactions, and Function

DNA Triplexes: Solution Structures, Hydration Sites, Energetics, Interactions, and Function

UV spectroscopic identification and thermodynamic analysis of protonated third strand deoxycytidine residues at neutrality in the triplex d(C+-T)6:[d(A-G)6d(C−-T)6]; evidence for a proton switch

Recognition and regulation of unique nucleic acid structures by small molecules

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UV spectroscopic identification and thermodynamic analysis of protonated third strand deoxycytidine residues at neutrality in the triplex d(C⁺-T)6:[d(A-G)6d(C⁻-T)6]; evidence for a proton switch