DNA backbone conformation in cis–syn pyrimidine[]pyrimidine cyclobutane dimers

Broyde, Suse; Stellman, Steven D.; Hingerty, Brian E.

doi:10.1002/bip.1980.360190913

Cited by 27 publications

(17 citation statements)

References 26 publications

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“…We believe that the explanation of these seemingly contradictory observations lies in the relative stability of the conformation induced in DNA by the dimer and that most of the contacts crucial for photolyase binding lie on the dimer-containing strand. Many of the altered torsion angles predicted in the model of dimercontaining double-stranded DNA were originally observed by Broyde et al (2) in an energy-minimized model of single-stranded dimer-containing DNA; thus, the conformation induced by the dimer may be the energetically favored one for both single-and double-stranded DNA because of the inherent restriction of bond rotation in the sugar-phosphate backbone (28). This interpretation is consistent with our demonstration that E. coli photolyase binds with approximately equal affinity to double-or single-stranded DNA (41).…”

Section: Discussionmentioning

confidence: 72%

Photolyases from Saccharomyces cerevisiae and Escherichia coli recognize common binding determinants in DNA containing pyrimidine dimers.

Baer

Sancar

1989

Mol. Cell. Biol.

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DNA photolyases catalyze the light-dependent repair of pyrimidine dimers in DNA. The results of nucleotide sequence analysis and spectroscopic studies demonstrated that photolyases from Saccharomyces cerevisiae and Escherichia coli share 37% amino acid sequence homology and contain identical chromophores. Do the similarities between these two enzymes extend to their interactions with DNA containing pyrimidine dimers, or does the organization of DNA into nucleosomes in S. cerevisiae necessitate alternative or additional recognition determinants? To answer this question, we used chemical and enzymatic techniques to identify the contacts made on DNA by S. cerevisiae photolyase when it is bound to a pyrimiidine dimer and compared these contacts with those made by E. coli photolyase and by a truncated derivative of the yeast enzyme when bound to the same substrate. We found evidence for a common set of interactions between the photolyases and specific phosphates in the backbones of both strands as well as for interactions with bases in both the major and minor grooves of dimer-containing DNA. Superimposed on this common pattern were significant differences in the contributions of specific contacts to the overall binding energy, in the interactions of the enzymes with groups on the complementary strand, and in the extent to which other DNA-binding proteins were excluded from the region around the dimer. These results provide strong evidence both for a conserved dimer-binding motif and for the evolution of new interactions that permit photolyases to also act as accessory proteins in nucleotide excision repair. The locations of the specific contacts made by the yeast enzyme indicate that the mechanism of nucleotide excision repair in this organism involves incision(s) at a distance from the pyrimidine dimer.Since its initial description in 1949, photoreactivation of UV-induced DNA damage has been characterized in a wide variety of organisms, including bacteria, fungi, plants, invertebrates, and all major groups of vertebrates except placental mammals (for reviews, see references 13, 33, 36, and 48). Enzymatic photoreactivation is carried out by DNA photolyases that bind to cis-syn cyclobutane dipyrimidines (pyrimidine dimers) in DNA and subsequently absorb and utilize the energy in a photon of near-UV or visible light to cleave the cyclobutane ring in a reaction that regenerates two intact pyrimidine monomers (26,27,42). A variety of in vivo and in vitro studies indicate that DNA photolyases have a number of properties in common: (i) they bind specifically and exclusively to pyrimidine dimers in DNA (13, 48); (ii) they are relatively insensitive to the sequence context in which the dimer is embedded (23, 25, 26); (iii) the enzymes interact with components of the endogenous nucleotide excision repair pathways to increase the efficiency of dimer excision in the dark (14, 30, 37, 54); and (iv) they bind specific cofactors that are the chromophores responsible for absorbing photoreactivating light (36). Nucleotide sequence ...

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Section: Discussionmentioning

confidence: 72%

Photolyases from Saccharomyces cerevisiae and Escherichia coli recognize common binding determinants in DNA containing pyrimidine dimers.

Baer

Sancar

1989

Mol. Cell. Biol.

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“…This suggests that much of the binding specificity conferred by interactions within the active site cavity arises from differences in the energy cost of flipping two unlinked bases versus a dimer. Several studies suggest that the presence of a dimer in a DNA helix weakens stacking interactions with adjacent bases and hydrogen bonding with the partners of the dimerized bases (27)(28)(29), and thus the energetic cost of flipping a dimer out of the helix and into the active site cavity should be lower than the cost of flipping two noncovalently linked pyrimidines. The free energy contributed by interactions between cavity residues and the dimer is sufficient to stabilize the dimer in the flipped state but is not sufficient to stabilize two noncovalently linked pyrimidine bases flipped out of the helix.…”

Section: A Model For Dimer Binding By Photolyase-approximatelymentioning

confidence: 99%

“…According to the model these residues contact regions immediately 5Ј to the dimer (Lys 383 ) or 3Ј to the dimer (Arg 452 and Gln 514 ). Both molecular modeling studies and NMR experiments suggest that in dimer-containing DNA the helix is distorted at the nucleotide 5Ј to the dimer and the first and second nucleotides 3Ј to the dimer (27,28,32). Thus there is an excellent correlation between the DNA sites that promote dimer-specific recognition and the location of photolyase residues that contribute to specific binding.…”

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confidence: 99%

Evidence for Dinucleotide Flipping by DNA Photolyase

Berg¹,

Sancar

1998

Journal of Biological Chemistry

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DNA photolyases repair pyrimidine dimers via a reaction in which light energy drives electron donation from a catalytic chromophore, FADH ؊ , to the dimer. The crystal structure of Escherichia coli photolyase suggested that the pyrimidine dimer is flipped out of the DNA helix and into a cavity that leads from the surface of the enzyme to FADH ؊ . We have tested this model using the Saccharomyces cerevisiae Phr1 photolyase which is >50% identical to E. coli photolyase over the region comprising the DNA binding domain. By using the bacterial photolyase as a starting point, we modeled the region encompassing amino acids 383-530 of the yeast enzyme. The model retained the cavity leading to FADH ؊ as well as the band of positive electrostatic potential which defines the DNA binding surface. We found that alanine substitution mutations at sites within the cavity reduced both substrate binding and discrimination, providing direct support for the dinucleotide flip model. The roles of three residues predicted to interact with DNA flanking the dimer were also tested. Arg 452 was found to be particularly critical to substrate binding, discrimination, and photolysis, suggesting a role in establishing or maintaining the dimer in the flipped state. A structural model for photolyase-dimer interaction is presented.Pyrimidine bases absorb strongly in the UV region and are highly susceptible to photochemical reactions that alter their structures. In DNA, cyclobutane pyrimidine dimers (CPDs) 1 and pyrimidine-pyrimidone (6-4) photoproducts are the most frequent and biologically significant products of these reactions. These lesions are lethal and mutagenic and must be repaired to ensure cell survival and genetic stability. DNA photolyases repair CPDs and (6-4) photoproducts via reactions in which near UV or visible light provides the energy for bond rearrangements which restore the pyrimidines to their undamaged state. Two types of DNA photolyases have been recognized with regard to substrate specificity as follows: cyclobutane dipyrimidine photolyases and (6-4) photolyases (see Ref. 1 for a recent review). Each type of enzyme recognizes and efficiently repairs a single type of damage (2, 3). The cyclobutane dipyrimidine photolyases, hereafter referred to as CPD photolyases, are the subject of this report.Understanding how the CPD photolyases efficiently repair pyrimidine dimers in DNA entails answering the following two questions: how do the enzymes recognize pyrimidine dimers specifically in the midst of a vast excess of nondamaged bases, and how do the enzymes catalyze dimer photolysis? Photolysis involves two noncovalently bound chromophores, reduced FAD and a second chromophore which, depending upon the source of the enzyme, is either folate or deazaflavin (4). Absorbance of a photon of photoreactivating light subsequent to substrate binding initiates electron donation by enzyme-bound FADH Ϫ to one of the bases in the dimer (4, 5). The photon may be absorbed either directly by FADH Ϫ or, more often, by the second chromophore w...

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“…The nucleoside samples were lyophilized twice and dissolved in 99.9% D20 to a concentration of 0.05 M. Metal ions were removed using Chelex-100 resin columns (Bio-Rad, Richmond, CA). Spectral analysis (LAOCOON 111) and computer simulated spectra were the final test of the chemical shift (6) and coupling constant ( J ) data listed in Tables 1 and 2. Pseudorotational parameters were calculated with the PSEUROT program (38) and are given in the relevant sections.…”

Section: Spectroscopic Measurementsmentioning

confidence: 99%

Characterization of thymidine ultraviolet photoproducts. Cyclobutane dimers and 5,6-dihydrothymidines

Cadet¹,

Voituriez²,

Hruska³

et al. 1985

Can. J. Chem.

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JEAN CADET, LUCIENNE VOITURIEZ, FRANK E. HRUSKA, LOU-SING KAN, FRANK A. A. M. DE LEEUW, and CORNELIS ALTONA. Can. J. Chem. 63, 2861Chem. 63, (1985.We describe the preparation of the six configurationally distinct cyclobutane-type photodimers generated by the acetonesensitized uv irradiation of thymidine in aqueous solution. Also prepared as minor photoproducts are the 5R and 5 S diastereoisomers of 5,6-dihydrothymidine, and two novel molecules, the 5R and 5.3 diastereoisomers of 5-acetonyl-5,6-dihydrothymidine. The purification of the ten molecules by chromatographic techniques (hplc, tlc) is described, along with their extensive characterization by uv, ir, cd, FAB-ms and 'H nmr. The proton chemical shifts and coupling constants are discussed in terms of the geometry of the pyrimidine, cyclobutane, and sugar rings. Les six diastCrCoisomkres possibles de la cyclobutidithymidine ont CtC prCparCs par photosensibilisation de la thymidine B la lumikre du proche ultra-violet en utilisant I'acetone. Les diastCrCoisomkres 5R et 5.3 de la dihydro-5,6 thymidine et deux nouveaux photoproduits, les formes 5R et 5 S de I'acCtonyl-5 dihydro-5,6 thymidine ont aussi CtC isolts. L'identification de ces photoproduits a fait appel B diverses techniques spectroscopiques: uv, ir, dichroi'sme circulaire, spectromktrie de masse par bombardement avec des atomes rapides et rmn 'H. Les valeurs des paramktres de rmn (deplacements chimiques, constantes de couplage) sont discutCes en termes de stCrCochimie des cycles pyrimidiniques, cyclobutyles et osidiques. IntroductionThe cyclobutane-type of photoproduct formed from adjacent thymine bases is the most thoroughly studied of the lesions induced by uv irradiation of DNA (1). The biological significance of these thymine photodimers is evidenced by the existence of mechanisms for their removal (2). Several studies reveal that the presence of the dimers leads to distortions in nucleic acid structure (3-7) that could play a role in the recognition by the enzymes of the repair system and may account for the altered specificity of, for example, restriction enzymes which employ DNA as a substrate (8). The numerous studies of the photodimerized thymine bases, Thy()Thy (R = H; Fig. I), have provided valuable photochemical and structural information (I), but relatively fewer data are available for the corresponding thymidine derivatives, dThd()dThd (R = 2-deoxy-P-D-ribose), which are the molecules of main interest in the present work. Wulff and Fraenkel (9) originally listed four isomeric forms of Thy()Thy. Actually, six configurationalIy-distinct forms are possible, since the trans-syn (ts) and cis-anti (ca) isomers exist as enantiomeric pairs ts 1, ts2 and c a l , ca2 whereas the cis-syn (cs) and trans-anti (ta) isomers exist as single (rneso) molecules. Similarly, six dThd()dThd are possible and are denoted CS, TS1, etc. according to the geometry of the Thy()Thy fragment (Fig. 1).

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DNA backbone conformation in cis–syn pyrimidine[]pyrimidine cyclobutane dimers

Cited by 27 publications

References 26 publications

Photolyases from Saccharomyces cerevisiae and Escherichia coli recognize common binding determinants in DNA containing pyrimidine dimers.

Photolyases from Saccharomyces cerevisiae and Escherichia coli recognize common binding determinants in DNA containing pyrimidine dimers.

Evidence for Dinucleotide Flipping by DNA Photolyase

Characterization of thymidine ultraviolet photoproducts. Cyclobutane dimers and 5,6-dihydrothymidines

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