Kinetics for exchange of the imino protons of the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix in complexes with the antibiotics netropsin and/or actinomycin

Pardi, Arthur; Morden, Kathleen M.; Patel, Dinshaw J.; Tinoco, Ignacio

doi:10.1021/bi00274a018

Cited by 51 publications

(34 citation statements)

References 20 publications

(30 reference statements)

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“…Recent crystallographic studies of distamycin A with d(CGCAAA1TJ7GCG)2 (7) revealed that the drug bound to a 5'-ATTT-3' sequence, although other sites with four A-T base pairs were available. Similar results have been obtained from footprinting (8,9), calorimetric (10), crystallographic (11)(12)(13)(14), and NMR (15)(16)(17)(18) studies of netropsin-DNA complexes. Analysis of these data indicates that van der Waals forces, hydrogen bonds, and electrostatic forces (19) contribute to the stability of these complexes and the sequence specificity of these drugs.…”

supporting

confidence: 80%

Structural characterization of a 2:1 distamycin A.d(CGCAAATTGGC) complex by two-dimensional NMR.

Pelton

Wemmer²

1989

Proc. Natl. Acad. Sci. U.S.A.

405

276

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Two-dimensional NMR has been used to study the 2:1 distamycin A-d(CGCAAATTGGC)-d(GCCAA-TTTGCG) complex. The nuclear Overhauser effect spectroscopy (NOESY) experiment was used to assign the aromatic and C1'H DNA protons and to identify drug-DNA contacts. These data indicate that two drug molecules bind simultaneously in the minor groove of the central 5'-AAATT-3' segment and are in close contact with both the DNA and one another. One drug binds with the formyl end close to the second adenine base of the A-rich strand, while the other drug binds with the formyl end close to the second adenine of the complementary strand. With this binding orientation, the positively charged propylamidinium groups are directed toward opposite ends of the helix. Molecular modeling shows that the minor groove must expand relative to the 1:1 complex to accommodate both drugs. Energy calculations suggest that electrostatic interactions, hydrogen bonds, and van der Waals forces contribute to the stability of the complex.An understanding of drug-DNA interactions at the molecular level is important in facilitating the design of new drugs and probes that can recognize specific DNA sequences. Distamycin A is an oligopeptide antibiotic ( Fig. 1) that binds preferentially to the minor groove of A+T-rich DNA sites (1, 2). Recently, several studies of 1:1 distamycin A-DNA complexes have provided insight into both the specificity and the forces responsible for the tight binding of this drug. Footprinting and affinity cleaving studies (3) have shown that distamycin A binds tightly to 5'-AAATT-3' in two orientations to a degree dependent on flanking base pairs and, in general, prefers sites that contain several adjacent adenine residues. NMR studies of distamycin A with d(CGCGAAT-TCGCG)2 (4, 5) have shown that 5'-AATT-3' is a good binding site, while calorimetric studies of distamycin A with d(GCGAATTCGC)2 (6) indicate that the binding constant for the complex is near 3 x 108 M-1, and that the binding process is enthalpy driven. Recent crystallographic studies of distamycin A with d(CGCAAA1TJ7GCG)2 (7) revealed that the drug bound to a 5'-ATTT-3' sequence, although other sites with four A-T base pairs were available. Similar results have been obtained from footprinting (8, 9), calorimetric (10), crystallographic (11)(12)(13)(14), and NMR (15-18) studies of netropsin-DNA complexes. Analysis of these data indicates that van der Waals forces, hydrogen bonds, and electrostatic forces (19) contribute to the stability of these complexes and the sequence specificity of these drugs.Using than the minimal four A-T base pairs was available. Titration of the DNA with distamycin A showed that at low drugto-DNA ratios at least two different binding sites were occupied. The binding behavior in this regime will be described elsewhere. At higher amounts of added drug, but still below a 1:1 ratio, a new binding mode was evident; a complex using this mode became the only form present at a drugto-DNA ratio of 2:1. It is the structure of this 2:1 complex whic...

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supporting

confidence: 80%

Structural characterization of a 2:1 distamycin A.d(CGCAAATTGGC) complex by two-dimensional NMR.

Pelton

Wemmer²

1989

Proc. Natl. Acad. Sci. U.S.A.

405

276

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“…But only two have been observed here, as elsewhere (21)(22)(23). A number of possibilities have been considered to account for this: for a rare tautomer we could observe tither (a) the hydroxyl and imino proton with the 6 amino protons being very broad via same exchange mechanism or (b) we could see the 6 mino protons with the others exchange broadened, while for the wobble structure we could observe either (c) the two iminos protons or (d) only the 6 amino protons.…”

Section: Discussionqsupporting

confidence: 53%

Comparison of the conformation of an oligonucleotide containing a central G-T base pair with the non-mismatch sequence by proton NMR

Quignard¹,

Fazakerley²,

Marel

et al. 1987

Nucl Acids Res

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We have recorded NOESY spectra of two non-selfcomplementary undecanucleotide duplexes. Frma the observed NOEs we do not detect any significant distortion of the helix when a 6-C pair is replaced by a G-T pair and the normal interresidue connectivities can be followed through the mismatch site. We conclude that the 2D spectra of the non-exchangeable protons do not allow differentiation between a wobble or rare tautmer form for the mismatch. NOE measurements in HIO, however, clearly show that the mismatch adopts a wobble structure and give information on the hydration in the minor groove for the G-T base pair which is embedded between two A-T base pairs in the sequence.

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“…The imino protons can recover their magnetization after saturation by spin-lattice relaxation (magnetic contribution) and by exchange with unperturbed solvent water (chemical contribution). Previous studies on transfer RNA (11,23,24) and DNA fragments (13)(14)(15)(16)(17) have demonstrated that the magnetic contribution predominates below room temperature and has a small activation energy, whereas the chemical contribution predominates above room temperature and has a large activation energy. We have determined the temperature dependence of the saturation recovery lifetimes of the AATT 12-mer duplex and the TATA 12-mer duplex between 0C and 60'C, and these are tabulated in Table 1.…”

Section: Bmentioning

confidence: 98%

Sequence dependence of hydrogen exchange kinetics in DNA duplexes at the individual base pair level in solution.

Patel¹,

Ikuta²,

Kozlowski³

et al. 1983

Proc. Natl. Acad. Sci. U.S.A.

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The kinetics for hydrogen exchange at individual base pairs in self-complementary deoxydodecanucleotide duplexes have been estimated from NMR saturation recovery measurements on the resolved imino protons as a function of temperature.The imino protons of dA-dT base pairs in the center of the fully alternating d(C-G-C-G-T-A-T-A-C-G-C-G) duplex exchange a factor of 2-to 3-fold faster than the corresponding protons at the same positions in the partially alternating d(C-G-C-G-A-A-T-T-C-G-C-G) duplex. These exchange parameters are a direct measure of the rate constants for transient opening of individual dA-dT base pairs in the dodecanucleotide duplexes and demonstrate faster opening kinetics for the "TATA" box region compared to the related "AATT" segment.Recent advances in oligonucleotide synthesis have led to the preparation of milligram quantities of DNA fragments of precise sequence containing at least one turn of helix (1). One such example is the self-Scheme I which has been extensively analyzed by single-crystal x-ray analysis in the solid state (2) and high-resolution NMR spectroscopy in aqueous solution (3). Both techniques have established that the central A-T-rich tetranucleotide segment shows conformational polymorphism in the duplex state as a function of temperature and solvent (2, 3).These observations initiated the present experiments, which probe the effect of sequence on the conformation and dynamics of DNA duplexes in solution. The completely alternating self-was synthesized by solid-state methods, and the effect of sequence variations in the center of the duplex was probed by comparative studies of the AATT 12-mer and TATA 12-mer duplexes.Redfield et al. have introduced nuclear Overhauser effect (NOE) and saturation recovery methods to probe the conformation and dynamics of transfer RNA in solution (4). They have demonstrated intra-and inter-base-pair NOEs involving exchangeable and nonexchangeable protons and have correlated the magnitude of the NOE effect with the inverse sixth power dependence of the interproton distance between the saturated and observed resonances. This distance-measuring methodology has wide applications, including its extension to elucidate conformational features of DNA fragments (3), synthetic DNAs (5), and antibiotic-DNA complexes (6) in solution.Hydrogen-deuterium exchange stop-flow measurements have demonstrated that the exchange kinetics of the Watson-Crick imino protons are sensitive markers of the dynamics of base pair opening in the interior of nucleic acid duplexes (7). NMR also can monitor hydrogen exchange, and the early research focused on line width changes of the exchangeable imino protons in the continuous wave mode to evaluate the kinetics of base pair-opening reactions (8, 9). The introduction of Fourier transform methods with H20 solvent suppression (10) readily permitted the incorporation of variable time delays between the saturation and observation pulses to monitor the kinetics of magnetization recovery. The initial measurements were made on...

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Kinetics for exchange of the imino protons of the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix in complexes with the antibiotics netropsin and/or actinomycin

Cited by 51 publications

References 20 publications

Structural characterization of a 2:1 distamycin A.d(CGCAAATTGGC) complex by two-dimensional NMR.

Structural characterization of a 2:1 distamycin A.d(CGCAAATTGGC) complex by two-dimensional NMR.

Comparison of the conformation of an oligonucleotide containing a central G-T base pair with the non-mismatch sequence by proton NMR

Sequence dependence of hydrogen exchange kinetics in DNA duplexes at the individual base pair level in solution.

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