X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature 1 1Edited by T. Richmond

Shatzky-Schwartz, Michal; Arbuckle, N.; Eisenstein, Miriam; Rabinovich, D.; Bareket‐Samish, Avital; Haran, Tali E.; Luisi, Ben F.; Shakked, Zippora

doi:10.1006/jmbi.1996.0878

Cited by 110 publications

(130 citation statements)

References 77 publications

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“…The magnitude of curvature in each of the three helices is close to 10°per decameric repeat and partitioned evenly along the double helix. This value compares well with data obtained from solution studies on similar sequence motifs (10). Analysis of the helical parameters at the base Thirty-base pair-long helices of CCGAATTCGG͞CCGAATTCG-G͞CCGAATTCGG based on the central 10 base pairs of each molecule of ACCGAATTCGGT.…”

Section: Resultssupporting

confidence: 82%

“…It should be noted, however, that in most of the reported AATT structures, the minor-groove bend at the central region is masked by another bend induced by crystal packing interactions. As a result, the overall curvature in these molecules is asymmetric and 90°away from the direction found in solution studies as discussed (10). Fig.…”

Section: Resultsmentioning

confidence: 73%

“…However, the E2 binding sites in the human papillomavirus (HPV) genomes, including the cancer-related strains HPV-16 and HPV-18 (9), exhibit a further level of specificity in the interaction with their cognate E2 proteins. This specificity is manifested by the identity of the central 4-bp region (e.g., AATT, AAAA͞TTTT), which is of the kind known to induce DNA curvature in solution (1,10), and by the corresponding binding affinities (11)(12)(13)(14)(15). Unlike HPV, in other papillomaviruses such as the well-studied bovine papillomavirus type 1 (BPV-1), the central region is highly variable (16).…”

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confidence: 99%

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DNA bending by an adenine–thymine tract and its role in gene regulation

Hizver

Rozenberg

Frolow

et al. 2001

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

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140

153

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To gain insight into the structural basis of DNA bending by adenine-thymine tracts (A-tracts) and their role in DNA recognition by gene-regulatory proteins, we have determined the crystal structure of the high-affinity DNA target of the cancer-associated human papillomavirus E2 protein. The three independent B-DNA molecules of the crystal structure determined at 2.2-Å resolution are examples of A-tract-containing helices where the global direction and magnitude of curvature are in accord with solution data, thereby providing insights, at the base pair level, into the mechanism of DNA bending by such sequence motifs. A comparative analysis of E2-DNA conformations with respect to other structural and biochemical studies demonstrates that (i) the A-tract structure of the core region, which is not contacted by the protein, is critical for the formation of the high-affinity sequence-specific protein-DNA complex, and (ii) differential binding affinity is regulated by the intrinsic structure and deformability encoded in the base sequence of the DNA target.A-tract ͉ papillomavirus E2-DNA target ͉ transcriptional control T he relationship between DNA sequence, structure, and function has been studied and discussed extensively for the last 20 years. A particular effort has been directed toward the structural elucidation of short runs of four to six adeninethymine residues, known as A-tracts, in an attempt to reveal the structural basis of DNA curvature induced by such sequence motifs when they are inserted in phase with the helical periodicity (1, 2). Despite numerous efforts, including x-ray crystallographic and solution studies, the structural basis of A-tractinduced bending has remained enigmatic (3). Because no single structure could explain the whole phenomenon, it was necessary to rely on models, several of which had been proposed (4). They generally conform to the gel migration data, which suggest that the center of curvature is toward the minor groove of the A-tracts and toward the major groove of the intervening general sequences (5). However, they differ substantially in the details of the stereochemical origin of curvature. This issue is of particular biological significance, as sequence-dependent DNA curvature or bending is an important determinant of DNA recognition by proteins (6).The E2 regulatory system of human papillomaviruses provides an example where sequence-specific binding of proteins to A-tracts is crucial to the organism's life cycle. The E2 proteins from all viral strains activate or repress transcription in a context-dependent manner and are required for the initiation of replication in vivo. Their function depends on sequence-specific binding to a highly conserved 12-bp sequence of the general form ACCGNNNNCGGT, where N4 is variable (7,8). However, the E2 binding sites in the human papillomavirus (HPV) genomes, including the cancer-related strains HPV-16 and HPV-18 (9), exhibit a further level of specificity in the interaction with their cognate E2 proteins. This specificity is manifested by th...

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Section: Resultssupporting

confidence: 82%

Section: Resultsmentioning

confidence: 73%

mentioning

confidence: 99%

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DNA bending by an adenine–thymine tract and its role in gene regulation

Hizver

Rozenberg

Frolow

et al. 2001

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

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140

153

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“…The large propeller twisting observed for the adenine residues within the A tracts themselves accounts in part for the observed rigidity (7). The X-ray crystal structures of oligo(dA)‚oligo(dT) and A n T n tracts reveal that this propeller twisting of the adenine residues may be stabilized by the formation of a cross-strand three-centered H-bond between the exocyclic N6 amino group of the adenosine and the C4 carbonyl group of the thymidine residues ( Figure 1) (4,6,8). NMR characterization of a DNA duplex containing an A 3 T 3 1 tract detected elevated activation enthalpies and entropies of amino group rotation for the central A5 residue, consistent with the formation of a threecentered H-bond (9).…”

mentioning

confidence: 97%

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

Mukerji

Williams

2001

Biochemistry

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The presence of A n and A n T n tracts in double-helical sequences perturbs the structural properties of DNA molecules, resulting in the formation of an alternate conformation to standard B-DNA known as B‘-DNA. Evidence for a transition occurring prior to duplex melting in molecules containing A n tracts was previously detected by circular dichroism (CD) and calorimetric studies. This premelting transition was attributed to a conformational change from B‘- to B-DNA. Structural features of A n and A n T n tracts revealed by X-ray crystallography include a large degree of propeller twisting of adenine bases, narrowed minor grooves, and the formation of three-centered H-bonds between dA and dT bases. We report UV resonance Raman (UVRR) and CD spectroscopic studies of two related DNA dodecamer duplexes, d(CGCAAATTTGCG)2 (A3T3) and d(CGCATATATGCG)2 [(AT)3]. These studies address the presence of three-centered H-bonds in the B‘ conformation and gauge the impact of these putative H-bonds on the structural and thermodynamic properties of the A3T3 duplex. UVRR and CD spectra reveal that the premelting transition is only observed for the A3T3 duplex, is primarily localized to the dA and dT bases, and is associated with base stacking interactions. Spectroscopic changes associated with the premelting transition are not readily detectable for the sugar−phosphate backbone or the cytosine and guanosine bases. The temperature-dependent concerted frequency shifts of dA exocyclic NH2 and dT C4O vibrational modes suggest that the A3T3 duplex forms three-centered hydrogen bonds at low temperatures, while the (AT)3 duplex does not. The enthalpy of this H-bond, estimated from the thermally induced frequency shift of the dT C4O vibrational mode, is approximately 1.9 kJ/mol or 0.46 kcal/mol.

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“…A large proportion of the substitution mutations were near adeninethymine tracts (AAAA, TTTT, or AATT sequences), known as A tracts, which are associated with alterations in nucleic acid conformation that include bends and a narrowed minor groove (27)(28)(29)(30). and pMP1 expresses the green fluorescent protein gene (GFP).…”

mentioning

confidence: 99%

Y586F mutation in murine leukemia virus reverse transcriptase decreases fidelity of DNA synthesis in regions associated with adenine–thymine tracts

Zhang

Svarovskaia²,

Barr³

et al. 2002

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

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Using in vivo fidelity assays in which bacterial ␤-galactosidase or green fluorescent protein genes served as reporters of mutations, we have identified a murine leukemia virus (MLV) RNase H mutant (Y586F) that exhibited an increase in the retroviral mutation rate Ϸ5-fold in a single replication cycle. DNA-sequencing analysis indicated that the Y586F mutation increased the frequency of substitution mutations 17-fold within 18 nt of adenine-thymine tracts (AAAA, TTTT, or AATT), which are known to induce DNA bending. Sequence alignments indicate that MLV Y586 is equivalent to HIV-1 Y501, a component of the recently described RNase H primer grip domain, which contacts and positions the DNA primer strand near the RNase H active site. The results suggest that wild-type reverse transcriptase (RT) facilitates a specific conformation of the template-primer duplex at the polymerase active site that is important for accuracy of DNA synthesis; when an adeninethymine tract is within 18 nt of the polymerase active site, the Y586F mutant RT cannot facilitate this specific template-primer conformation, leading to an increase in the frequency of substitution mutations. These findings indicate that the RNase H primer grip can affect the template-primer conformation at the polymerase active site and that the MLV Y586 residue and template-primer conformation are important determinants of RT fidelity. R everse transcriptase (RT), which copies retroviral genomic RNA into double-stranded DNA during reverse transcription, contains two major enzymatic activities: a DNA polymerase activity that uses either RNA or DNA as a template and an RNase H activity that can degrade RNA in an RNA⅐DNA hybrid (1). The crystal structure of HIV-1 RT in complex with a template-primer and a dNTP substrate has shown that the polymerase active site and the RNase H cleavage site are separated by 18 nt of the template-primer (2). In the case of murine leukemia virus (MLV) RT, the DNA polymerase and RNase H activities reside in physically separable domains of a single monomeric protein (3).The RNase H activity of all retroviral RTs performs several functions that are essential for the viral life cycle (4), which include degradation of the RNA template after synthesis of the minusstrand DNA, generation of a specific polypurine primer from which plus-strand DNA synthesis initiates, subsequent removal of the polypurine primer to complete synthesis of the viral doublestranded DNA, and removal of the minus-strand tRNA primer (5). During minus-strand DNA synthesis, RT positions the RNase H active site and cleaves the RNA Ϸ18 nt 3Ј of the site of DNA synthesis (6).All retroviral RTs carry out error-prone DNA synthesis, in part because they lack a proofreading activity and possess a low affinity for the template (7). The low fidelity of retroviral replication is a major force for generation of high levels of variation in retroviral populations (8), which allows them to adapt quickly to changes in their environment. One important outcome of this high adaptability is t...

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X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature 1 1Edited by T. Richmond

Cited by 110 publications

References 77 publications

DNA bending by an adenine–thymine tract and its role in gene regulation

DNA bending by an adenine–thymine tract and its role in gene regulation

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

Y586F mutation in murine leukemia virus reverse transcriptase decreases fidelity of DNA synthesis in regions associated with adenine–thymine tracts

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X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature 1 1Edited by T. Richmond

Cited by 110 publications

References 77 publications

DNA bending by an adenine–thymine tract and its role in gene regulation

DNA bending by an adenine–thymine tract and its role in gene regulation

UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A3T3 Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds

Y586F mutation in murine leukemia virus reverse transcriptase decreases fidelity of DNA synthesis in regions associated with adenine–thymine tracts

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UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A₃T₃ Tract: Evidence for a Premelting Transition and Three-Centered H-Bonds