1
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Structural evidence of anti-HIV lectin actinohivin specific to HMTG of gp120. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312096973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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2
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Damaged guanine residue relevant to gastrointestinal cancer allows thymine residue to be flexible between Watson–Crick type pairing and large wobbling. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312096791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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3
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Crystal structures of DNA containing X relevant to gastro-intestinal cancer. Acta Crystallogr A 2011. [DOI: 10.1107/s010876731109283x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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4
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Specificity and efficiency in activity of anti-HIV actinohivin for sugar binding. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311092841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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5
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Structure determination (2) of anti-HIV actinohivin in complex with mannobioses. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311092580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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6
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Crystal structure of α-carbonic anhydrase from Chlamydomonas reinhardtii. Acta Crystallogr A 2007. [DOI: 10.1107/s0108767307097437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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7
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Two different lipoamide dehydrogenases (E 3s) from Thermus thermophilus: crystal structures and their evolutionary relationship. Acta Crystallogr A 2006. [DOI: 10.1107/s0108767306097248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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8
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9
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Structural basis for antigene and antisense duplexes with modified nucleotides. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305097461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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10
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Crystal structures of uricase complexed with its real substrate and product. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305079535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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11
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X-ray analyses of DNA dodecamers containing 2'-deoxy-5-formyluridine. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Crystal structure of Sulfolobus tokodaiiaspartyl-tRNA synthetase. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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13
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Preliminary X-ray analysis of RNA oligomers containing CUG repeats. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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14
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Crystal structure of a reaction intermediate of pyruvate oxidase from Aerococcus viridans. Acta Crystallogr A 2004. [DOI: 10.1107/s0108767304097570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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15
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Roles of the base-stacked XYYX in forming multiple associations of the base-intercalated duplexes. Acta Crystallogr A 2004. [DOI: 10.1107/s0108767304097466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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16
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Mutants at the 4th and 5th positions of the sequence d(gcGXYAgc) suggest a variety of the DNA octaplex. Acta Crystallogr A 2004. [DOI: 10.1107/s0108767304099611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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17
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Abstract
The structural compositions of the most active deoxyribozyme and its derivatives have been examined by electrophoresis, and their crystallization conditions were surveyed for X-ray analysis. It has been found that Mg2+ ion is essential to form the active binary complex between the catalytic DNA and the substrate, and that heat-treatment is effective to prevent formation of the inactive quaternary complex between the two enzymes and the two substrates. Crystals obtained by the hanging drop vapor diffusion method are composed of the active binary complex.
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18
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X-ray analyses of two DNA dodecamers containing N4-methoxy-cytosine paired with adenine or guanine. NUCLEIC ACIDS SYMPOSIUM SERIES 2003:239-40. [PMID: 12903357 DOI: 10.1093/nass/44.1.239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To investigate mismatch of base-pairings in relation to mutagenesis by oxyamines, crystal structures of two DNA dodecamers with the sequence d(CGCZAA TTmo4CGCG) (Z = A or G), containing N4-methoxy-cytosine (mo4C), have been determined by X-ray analysis. These dodecamers essentially form right-handed B-form duplexes, respectively. In the dodecamer with Z = A, the two mo4C residues are adapted in imino form with the anti methoxyl group to form pairs with A on the opposite strand in a manner of Watson-Crick fashion. While in the dodecamer with Z = G, one mo4C in amino form with the anti methoxyl group forms a normal Watson-Crick pair with G, but the other one in imino form with syn methoxyl conformation wobbles with G. Based on these results, possible mutation mechanism has been proposed.
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19
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X-ray analyses of d(GCGAAAGC) and d(GXGAAAGCT), where X = 2'-deoxy-5-iodocytidine. NUCLEIC ACIDS RESEARCH. SUPPLEMENT (2001) 2003:191-2. [PMID: 12836329 DOI: 10.1093/nass/1.1.191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
DNA fragments containing a sequence d(GCGAAAGC) are known to be highly thermostable. To investigate the structural basis for such a specific property, crystallographic studies of the DNA octamer and a nanomer d(GXGAAAGCT) (X = 2'-deoxy-5-iodocytidine) have been performed. The present higher resolution X-ray analyses have shown that both DNA oligomers are stabilized respectively to form a zipper-type duplex homodimer. PAGE of these oligomers, however, indicates that they are monomeric even when their crystals were dissolved at room temperature.
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20
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X-ray analyses of DNA dodecamers containing 2'-deoxy-5-formyluridine. NUCLEIC ACIDS RESEARCH. SUPPLEMENT (2001) 2003:279-80. [PMID: 12836373 DOI: 10.1093/nass/1.1.279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
It is known that formylation of thymine base induces purine transition in DNA replication. In order to establish the structural basis for such mutagenesis, crystal structures of two kinds of DNA dodecamers d(CGCGRATf5UCGCG) with f5U = 2'-deoxy-5-formyluridine and R = A or G have been determined. The f5U residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble) with G, the latter being the first example. Structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.
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21
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X-ray analysis of d(GCGAACGC); intra-duplex and inter-duplex hand-in-pocket motifs. NUCLEIC ACIDS RESEARCH. SUPPLEMENT (2001) 2003:199-200. [PMID: 12836333 DOI: 10.1093/nass/1.1.199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The structure of DNA octamer with the sequence d(GCGAACGC) has been determined by the X-ray crystallography to investigate the specific DNA structural motifs that are useful for designing various functional DNA molecules. Two kinds of interaction motifs for the bulged out adenosine residues have been found. One is an intra-duplex and the other is an inter-duplex hand-in-pocket motif. These interactions consist of the novel A:G pairs that have never been found so far in any crystal and solution studies on DNA molecules.
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22
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Crystallographic studies on damaged DNAs IV. N( 4)-methoxycytosine shows a second face for Watson-Crick base-pairing, leading to purine transition mutagenesis. Nucleic Acids Res 2001; 29:3949-54. [PMID: 11574676 PMCID: PMC60249 DOI: 10.1093/nar/29.19.3949] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To investigate the mutation mechanism of purine transitions in DNA damaged with methoxyamine, a DNA dodecamer with the sequence d(CGCAAATTmo(4)CGCG), where mo(4)C is 2'-deoxy-N(4)-methoxycytidine, has been synthesized and the crystal structure determined by X-ray analysis. The duplex structure is similar to that of the original undamaged B-form dodecamer, indicating that the methoxylation does not affect the overall DNA conformation. Electron density maps clearly show that the two mo(4)C residues form Watson-Crick-type base pairs with the adenine residues of the opposite strand and that the methoxy groups of mo(4)C adopt the anti conformation to N(3) around the C(4)-N(4) bond. For the pair formation through hydrogen bonds the mo(4)C residues are in the imino tautomeric state. Together with previous work, the present work establishes that the methoxylated cytosine residue can present two alternate faces for Watson-Crick base-pairing, thanks to the amino<-->imino tautomerism allowed by methoxylation. Based on this property, two gene transition routes are proposed.
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23
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Crystallographic studies on damaged DNAs: III. N(4)-methoxycytosine can form both Watson-Crick type and wobbled base pairs in a B-form duplex. J Biochem 2001; 130:9-12. [PMID: 11432773 DOI: 10.1093/oxfordjournals.jbchem.a002967] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To investigate the mutation mechanism of purine transition in DNA damaged with methoxyamine, a DNA dodecamer with the sequence d(CGCGAATTmo(4)CGCG), where mo(4)C is 2'-deoxy-N(4)-methoxycytidine, has been synthesized and its crystal structure determined. Two dodecamers form a B-form duplex. Electron density maps clearly show that one of the two mo(4)C residues forms a pair with a guanine residue of the opposite strand, the geometry being the canonical Watson-Crick type, and that the other mo(4)C residue forms a wobble pair with the opposite guanine residue. These two pairings are ascribed to the tautomerization of the methoxylated cytosine moieties between the amino and imino forms.
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24
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X-ray analysis of a DNA dodecamer containing 5-formyluracil. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300025848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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25
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Crystal structures of DNAs damaged by methoxylation reveal the reason why pyrimidine transition and purine transition occur during replication. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300025836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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26
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X-ray analysis of a DNA dodecamer containing 2'-deoxy-N4-methoxycytidine. NUCLEIC ACIDS SYMPOSIUM SERIES 2000:49-50. [PMID: 10780373 DOI: 10.1093/nass/42.1.49] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The crystal structure of DNA dodecamer with the sequence of d(CGCAAATTXGCG), where X is 2'-deoxy-N4-methoxycytidine, has been determined by X-ray analysis. The dodecamers form a double helix with B-form conformation. The electron density indicates that the two modified cytosine bases respectively make a pair with the adenine bases on the opposite strand in a manner of Watson-Crick geometry and that the methoxy groups are in anti conformation to the N3 atom.
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N6-methoxyadenine in damaged DNA has two faces in property of Watson-Crick base pairing. NUCLEIC ACIDS SYMPOSIUM SERIES 2000:121-2. [PMID: 10780409 DOI: 10.1093/nass/42.1.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
In order to investigate mutation mechanism with oxyamine, two DNA dodecamers containing 2'-deoxy-N6-methoxyadenosine have been synthesized and their crystal structures have been determined. The dodecamers are associated in B form duplexes. The methoxy groups attached to the adenine bases do not affect the DNA conformation significantly. Electron densities clearly show that N6-methoxyadenine moiety forms Watson-Crick type pairing with both, thymine and cytosine bases. Such two faces in pairing are the origin of pyrimidine transition mutation.
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Crystallographic studies on damaged DNAs. I. An N(6)-methoxyadenine residue forms a Watson-Crick pair with a cytosine residue in a B-DNA duplex. J Mol Biol 1999; 294:1215-22. [PMID: 10600379 DOI: 10.1006/jmbi.1999.3303] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Oxyamines such as hydroxylamine and methoxylamine disturb DNA replication and act as potent mutagens, causing nucleotide transition from one purine to another or one pyrimidine to another. In order to investigate mismatch base-pairing in DNA damaged with oxyamines, a dodecamer with the sequence d(CGCGmo(6)AATCCGCG), where mo(6) A is 2'-deoxy-N(6)-methoxyadenosine, was synthesized and its crystal structure determined. No significant conformational changes are found between the present dodecamer and the original undamaged B-form dodecamer. Electron density maps clearly show that the mo(6)A residue forms a base-pair with a 2'-deoxycytidine residue through hydrogen bonds similar to a Watson-Crick G.C base-pair. For these hydrogen bonds to be made, N(6)-methoxyadenine must chemically take the imino form. The methoxylation thus enables the adenine base to mimic a guanine base. As a result, misincorporation of 2'-deoxycytidine instead of thymidine, or 2'-deoxyadenosine instead of 2'-deoxyguanosine, can occur in DNA replication.
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Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis. J Mol Biol 1999; 294:1223-30. [PMID: 10600380 DOI: 10.1006/jmbi.1999.3304] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In a previous paper, 2'-deoxy-N(6)-methoxyadenosine (mo(6)A) was shown to form a mismatch base-pair with 2'-deoxycytidine with a Watson-Crick-type geometry. To fully understand the structural basis of genetic mutations with damaged DNA, it is necessary to examine whether the methoxylated adenine residue still has the ability to form the regular Watson-Crick pairing with a thymine residue. Therefore, a DNA dodecamer with the sequence d(CGCGmo(6)AATTCGCG) has been synthesized and its crystal structure determined. The methoxylation has no significant effect on the overall DNA conformation, which is that of a standard B-form duplex. The methoxylated adenine moieties adopt the amino tautomer with an anti conformation around the C(6)-N(6) bond to the N(1) atom, and they form a Watson-Crick base-pair with thymine residues on the opposite strand, similar to an unmodified adenine residue. It is concluded that methoxylated adenine can present two alternate faces for base-pairing, thanks to the amino<-->imino tautomerism allowed by methoxylation. Based on this property, two gene transition routes are proposed.
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