X-ray structure of the DNase I-d(GGTATACC)2 complex at 2·3Å resolution

Weston, Simon A.; Lahm, Armin; Suck, Dietrich

doi:10.1016/0022-2836(92)91064-v

Cited by 250 publications

(227 citation statements)

References 42 publications

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“…Similarly, the observed binding enthalpy can be parsed into two contributions: (3) whereΔH pe is assumed to be essentially zero [53], and ΔH t equal to ΔH obs . For poly(dA)·poly (dT) binding with DB75, ΔH t was obtained as 3.1 kcal mol −1 , while for poly(dA-dT)·poly(dAdT) binding with DB75, ΔH t was obtained as −4.5 kcal mol −1 .…”

Section: Discussionmentioning

confidence: 99%

“…As shown by DNA footprinting methods, well-characterized and structurally-diverse compounds, such as netropsin, Hoechst 33258 and berenil, which bind at AT sites in the DNA minor groove, can interact with a large variety of AT sequences [1,2]. For compounds of this size, a site of at least four base pairs in length is required but the affinities of the compounds for different AT sites can vary by a surprisingly large amount [3][4][5]. Early studies of netropsin binding to synthetic polydeoxyribonucleotides by Zimmer and coworkers [6,7] revealed sequence dependent differences in affinities and complex structures.…”

Section: Introductionmentioning

confidence: 99%

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Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

Liu

Kumar

Boykin

et al. 2007

Biophysical Chemistry

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With the goal of developing a better understanding of the antiparasitic biological action of DB75, we have evaluated its interaction with duplex alternating and nonalternating sequence AT polymers and oligomers. These DNAs provide an important pair of sequences in a detailed thermodynamic analysis of variations in interaction of DB75 with AT sites. The results for DB75 binding to the alternating and nonalternating AT sequences are quite different at the fundamental thermodynamic level. Although the Gibbs energies are similar, the enthalpies for DB75 binding with poly(dA)·poly (dT) and poly(dA-dT)·poly(dA-dT) are +3.1 and −4.5 kcal/mole, respectively, while the binding entropies are 41.7 and 15.2 cal/mol·K, respectively. The underlying thermodynamics of binding to AT sites in the minor groove plays a key role in the recognition process. It was also observed that DB75 binding with poly(dA)·poly(dT) can induce T·A·T triplet formation and the compound binds strongly to the dT·dA·dT triplex.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

Liu

Kumar

Boykin

et al. 2007

Biophysical Chemistry

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“…Especially, ␤-hairpin region is suggested to be responsible for the determination of the substrate specificity by TRAS1-EN. The predicted DNA-binding model of TRAS1-EN, based on the DNase I-DNA complex (42), has been constructed (Fig. 6).…”

Section: Catalytic Sites Of Tras1-en Deduced From the Crystalmentioning

confidence: 99%

“…First, we made the plasmid DNA substrate, which includes the B. mori telomeric repeat sequence in the pGEM-T vector. Then the endonuclease activities of the purified EN proteins were optimized by measuring the abilities to convert supercoiled plasmid containing (TTAGG) 42 into open circle or linear DNA (Fig. 5B).…”

Section: Mutagenesis Studies Of Tras1-en Reveal the Telomeric Repeat-mentioning

confidence: 99%

Crystal Structure of the Endonuclease Domain Encoded by the Telomere-specific Long Interspersed Nuclear Element, TRAS1

Maita

Anzai

Aoyagi

et al. 2004

Journal of Biological Chemistry

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The telomere-specific long interspersed nuclear element, TRAS1, encodes an endonuclease domain, TRAS1-EN, which specifically cleaves the telomeric repeat targets (TTAGG) n of insects and (TTAGGG) n of vertebrates. To elucidate the sequence-specific recognition properties of TRAS1-EN, we determined the crystal structure at 2.4-Å resolution. TRAS1-EN has a four-layered ␣/␤ sandwich structure; its topology is similar to apurinic/ apyrimidinic endonucleases, but the ␤-hairpin (␤ 10 -␤ 11 ) at the edge of the DNA-binding surface makes an extra loop that distinguishes TRAS1-EN from cellular apurinic/apyrimidinic endonucleases. A protein-DNA complex model suggests that the ␤ 10 -␤ 11 hairpin fits into the minor groove, enabling interaction with the telomeric repeats. Mutational studies of TRAS1-EN also indicated that the Asp-130 and ␤ 10 -␤ 11 hairpin structure are involved in specific recognition of telomeric repeats.Non-long terminal repeat retrotransposons, also known as long interspersed nuclear elements (LINEs), 1 are transposable elements that encode a reverse transcriptase and insert into genomic locations via RNA intermediates. The recent progress of the human genome project has revealed that one LINE, L1, integrates throughout chromosomes and occupies more than 20% of the genome (1). The integration of L1 may play a role in genetic diseases and cancers (2) and in gene evolution and genome reconstruction (3-5).The LINEs have been classified into two types according to the number of open reading frames (ORFs) (6). The first type of element has a single ORF and encodes an endonuclease domain near its C terminus; this type of endonuclease (also known as restriction enzyme-like endonuclease) is similar in some residual motifs to various prokaryotic restriction enzymes (7). The second type of element has two ORFs; ORF1 encodes a retroviral Gag-like protein whose function is still unclear, and ORF2 encodes a protein with an endonuclease domain at its N terminus and a reverse transcriptase domain in the center of the ORF. This class of endonuclease domain is made up of about 250 amino acid residues and shares sequence homology with apurinic/apyrimidinic endonucleases (APE), such as human APE1 and Escherichia coli exonuclease III.Most of the APE-like endonuclease-encoding retrotransposons do not insert in a sequence-specific manner into the host genome, like the human L1 elements that cleave AT-rich sequences with a low sequence specificity (8). However, several endonuclease-encoding LINE have very restricted integration targets within the genome (9). TRAS1 and R1Bm, found in Bombyx mori, are the typical sequence-specific elements, which insert between T and A of the (TTAGG) n telomeric repeat and a specific site in 28 S rDNA of B. mori, respectively (10, 11). Recent studies have shown that the endonuclease domain in the ORF2 of TRAS1 (12) and R1Bm (13) determines its own target sequence recognition and DNA cleavage activity.The amino acid identity between human APE1 and the endonuclease domain of TRAS1 (TRAS1-EN) is n...

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“…Recently, trinucleotide bending propensity parameters were deduced from deoxyribonuclease I (DNase I) digestion data [1,2]. DNase I, an enzyme with no pronounced sequence specificity, bends DNA towards the major groove [3,4]. Since the cleavage rate is thought to primarily depend on the bendability of DNA in this direction [5], we consider these trinucleotide parameters as indicators of bendability, i.e.…”

Section: Introductionmentioning

confidence: 99%

Distribution of bending propensity in DNA sequences

Gabrielian¹,

Simoncsits²,

Pongor³

1996

FEBS Letters

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Local bending propensity and curvature of DNA can he characterized using a vector description of DNA bendability, based on a set of parameters derived from deoxyribonuclease I (DNase I) cleavage experiments. Two characteristics -arithmetic and vector averages of bendability -were successfully used to predict experimentally known bendable, rigid and curved segments in DNA. A characteristic distribution of bendability is conserved in evolutionarily related kinetoplast sequences. An analysis of the M. genitalium and H. influenzae genomes as well as fragments of human and yeast genomes shows, on the other hand, that highly curved segments -similar to artificially designed curved oligonucleotides -are extremely rare in natural DNA.bendable segments [2]. Bendability plots were drawn by first dividing a DNA sequence into overlapping trinucleotides, then assigning a bendability value given in Table 1 to the center of each trinucleotide. (In this way the first and last nucleotides will have no values so a sequence of 32 residues will have 30 values.) Average bendability and helical asymmetry (see below at Eq. 1) were calculated for segments of 32 bp, i.e. approximately three helical turns. The calculated profiles do not significantly depend on this window length. Random sequences were generated by random shuffling the sequence of entire genomes. The shuffled sequences were then divided into overlapping segments of 32 residues for the calculation of the values given in Table 1 which are averages and standard deviations calculated from 10 runs of randomization. Results and discussion

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X-ray structure of the DNase I-d(GGTATACC)2 complex at 2·3Å resolution

Cited by 250 publications

References 42 publications

Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove

Crystal Structure of the Endonuclease Domain Encoded by the Telomere-specific Long Interspersed Nuclear Element, TRAS1

Distribution of bending propensity in DNA sequences

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