The Anatomy of A-, B-, and Z-DNA

Dickerson, Richard E.; Drew, Horace R.; Conner, Benjamin N.; Wing, Richard M.; Fratini, Albert; Kopka, Mary L.

doi:10.1126/science.7071593

Cited by 644 publications

(381 citation statements)

References 57 publications

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“…If an amino acid side chain(s) in the 2.3-2.4 region makes a direct contact with the Ϫ11 adenine, then either the interaction involves the C2 hydrogen (a likely hydrophobic linkage) or the substitution of the C2 hydrogen causes a steric problem for the interaction. In B-DNA structure, the C2 hydrogen of an adenine is available in the minor groove (34). However, the line-up of base-edge interaction potential (with a protein) through the minor groove in an A:T base pair is practically the same as that in a T:A base pair: H bond acceptor-H atom-H bond acceptor (Fig.…”

Section: Role Of C2 Hydrogen Of Adenine At ϫ11 In Promoter Openingmentioning

confidence: 99%

An Unsubstituted C2 Hydrogen of Adenine Is Critical and Sufficient at the –11 Position of a Promoter to Signal Base Pair Deformation

Lee

Lim

2004

Journal of Biological Chemistry

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The conserved A:T base pair at the ؊11 position of the promoters in Escherichia coli is very sensitive to substitutions. In vitro transcription with the galP1 promoter having a natural or unnatural base in either strand at position ؊11 showed that only a purine base with no side group at C2 in the nontemplate strand is transcriptionally potent; neither a purine with an amino group at C2 nor a pyrimidine support transcription. The amino group at C6 in the omnipresent adenine at ؊11 does not play any role in promoting transcription. The nature of the base, complementary or noncomplementary, at ؊11 in the template strand also does not influence transcription. We propose that the adenine, by becoming extrahelical, interacts with an amino acid(s) of the 2.3-2.4 region of for which an unsubstituted C2 hydrogen is critical.Transcription initiation executed by a bacterial RNA polymerase holoenzyme (E) starts with its binding to a promoter DNA sequence (formation of a closed complex) and is followed by a multistep process leading to the formation of an open complex. The open complex is competent to initiate polymerization of ribonucleotides according to the DNA sequences of the template strand (1-4). Both DNA (Ϫ10 region of the promoter) and the multisubunit enzyme go through major conformational changes in becoming an open complex (4 -9). Although the exact structural changes that they undergo during open complex formation are unknown, recent crystallographic and fluorescence resonance energy transfer studies of various bacterial E and their parts provided some clue to the structure of the open complex (10 -15). It is believed that in a fully mature open complex, about 15 base pairs in DNA (from Ϫ12 to ϩ3 relative to the transcription start site) become single-stranded by the so-called "melting" process, which we will refer to as DNA deformation (16 -18). Several amino acid residues in the 2.3-2.4 region of the subunit were inferred to make consequential contacts with bases in the Ϫ10 region of the promoter: (4, 16, 18 -27). Although these amino acid residues were shown to strategically lie on one face of the subunit to be able to perform the two functions in open complex formation, RNA polymerase binding and DNA deformation (10, 11), the details of the interactions from structural viewpoints remain unknown. Studies of transcription initiation with specifically designed DNA templates suggested that DNA deformation nucleates at around position Ϫ10/Ϫ11 (9, 25-28). The omnipresent A:T base pair at the position Ϫ11 was specifically suggested to play a "master" role in signaling DNA deformation (29). We investigated the properties of the Ϫ11 base pair, which are critical in interacting with and in signaling base pair deformation. EXPERIMENTAL PROCEDURESIn Vitro Transcription Assay-In vitro transcription reactions were performed in a 25-l volume following the procedure of Choy and Adhya (30). The 70 -saturated RNA polymerase from Escherichia coli was purchased from Epicenter Technologies (Madison, WI). The reaction mixture (...

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Section: Role Of C2 Hydrogen Of Adenine At ϫ11 In Promoter Openingmentioning

confidence: 99%

An Unsubstituted C2 Hydrogen of Adenine Is Critical and Sufficient at the –11 Position of a Promoter to Signal Base Pair Deformation

Lee

Lim

2004

Journal of Biological Chemistry

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“…2). P and S values are shown in Table 1 (18,19). At the strong-stretching limit where P dominates the elasticity (x Ϸ 14-16 m), DNA follows the WLC behavior predicted by Eq.…”

Section: Behavior and Analysis Of Force-extension Curvesmentioning

confidence: 99%

Ionic effects on the elasticity of single DNA molecules

Baumann

Smith

Bloomfield

et al. 1997

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

924

111

996

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We used a force-measuring laser tweezers apparatus to determine the elastic properties of -bacteriophage DNA as a function of ionic strength and in the presence of multivalent cations. The electrostatic contribution to the persistence length P varied as the inverse of the ionic strength in monovalent salt, as predicted by the standard worm-like polyelectrolyte model. However, ionic strength is not always the dominant variable in determining the elastic properties of DNA. Monovalent and multivalent ions have quite different effects even when present at the same ionic strength. Multivalent ions lead to P values as low as 250-300 Å, well below the high-salt ''fully neutralized'' value of 450-500 Å characteristic of DNA in monovalent salt. The ions Mg 2؉ and Co(NH 3 ) 6 3؉ , in which the charge is centrally concentrated, yield lower P values than the polyamines putrescine 2؉ and spermidine 3؉ , in which the charge is linearly distributed. The elastic stretch modulus, S, and P display opposite trends with ionic strength, in contradiction to predictions of macroscopic elasticity theory. DNA is well described as a worm-like chain at concentrations of trivalent cations capable of inducing condensation, if condensation is prevented by keeping the molecule stretched. A retractile force appears in the presence of multivalent cations at molecular extensions that allow intramolecular contacts, suggesting condensation in stretched DNA occurs by a ''thermal ratchet'' mechanism.Ions strongly affect such biologically significant behavior of DNA as wrapping around nucleosomes, packaging inside bacteriophage capsids, and binding to proteins involved in transcriptional initiation and elongation. While such influence is often explained by relatively simple ion exchange equilibria (1, 2), in many cases ions appear to exert their effect by modifying the structure and mechanical properties of DNAits bending and torsional rigidity. The study of the ionic dependence of the elastic properties of DNA is therefore essential to understand the energetics of these key biological processes.Recent technical advances in nanomanipulation have allowed the mechanical behavior of single DNA molecules to be studied. Magnetic beads (3, 4), micro fibers (5), optical traps (6), and hydrodynamic flow (7) have been used to apply a wide range of forces to individual bacteriophage DNA molecules. Smith et al. (6) have recently described three regimes in the elastic response of -bacteriophage DNA ( DNA) molecules. Between 0.01 and 10 pN, the molecule behaves as an entropic spring and is well described by the worm-like chain (WLC) model (8-10), from which a persistence length, P, and a contour length, L o , can be obtained. Between 10 and 65 pN, the molecule deviates from the predictions of the inextensible WLC as it extends beyond its B-form contour length. From this ''enthalpic elasticity'' regime an elastic stretch modulus, S, can be obtained. Finally, at about 65 pN, the molecule suddenly yields in a highly cooperative fashion and overstretches Ϸ1....

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“…Since approx. 10 bp of Pu/Py is sufficient to permit Z formation (Singleton et al, 1983), there are at least two potential Z-form sites within this region in RU (9 and 15 bp) but only one in EXT because of a 12-bp deletion (the length of a single helical turn of Z-DNA; Dickerson et al, 1982). It is noteworthy that, except for two nucleotide substitutions that border the deletion in EXT, this segment along with 20 bp upstream and 30 bp downstream has been 100% conserved in RU and EXT .…”

Section: (C) Subclone Of a Repeating Pu:py Domainmentioning

confidence: 99%

Demonstration of remarkable sequence divergence in variants of a complex satellite DNA by molecular cloning

Stringfellow

Fowler

LaMarca

et al. 1985

Gene

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SUMMARYRepeat units of a complex G + C-rich satellite of the Bermuda land crab have been cloned by insertion into either the PstI or EcoRI site of pBR322 or the EcoRI site of pUC9. While most of the recombinants contained inserts of approx. 2.1 kb, the average size of repeat units seen in cellular satellite digests, several inserts were markedly different in size. Two domains that account for major sequence differences among the satellite variants and that may be 'hotspots' for sequence modification have been subcloned to permit characterization of their secondary and tertiary structures independent of the influence of the other unusual sequences present. One of these domains is striking in its content of simple repeats; one strand is highly biased in pyrimidines which may permit the formation of unusual secondary and/or tertiary conformations. The other subcloned domain is rich in Pu/Py; preliminary data indicate a transition from B-+Z DNA in this region.

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The Anatomy of A-, B-, and Z-DNA

Cited by 644 publications

References 57 publications

An Unsubstituted C2 Hydrogen of Adenine Is Critical and Sufficient at the –11 Position of a Promoter to Signal Base Pair Deformation

An Unsubstituted C2 Hydrogen of Adenine Is Critical and Sufficient at the –11 Position of a Promoter to Signal Base Pair Deformation

Ionic effects on the elasticity of single DNA molecules

Demonstration of remarkable sequence divergence in variants of a complex satellite DNA by molecular cloning

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