Molecular Replacement Using DNA Helical Symmetry

Baikalov, Igor; Dickerson, Richard E.

doi:10.1107/s0907444997010512

Cited by 3 publications

(7 citation statements)

References 18 publications

(19 reference statements)

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“…Further, the occupation of the special position (0, 0, z) in the cell provides clues about the molecular structure of C 4 A 2 C 4 A 2 and pointers for model building. Structure determination by the molecularreplacement method would involve only two unknowns, namely the rotation about and translation along c in the cell (Baikalov & Dickerson, 1998).…”

Section: Resultsmentioning

confidence: 99%

Crystallization and preliminary investigations on a telomeric repeat sequence C₄A₂C₄A₂

Savitha

Leonidas²,

Acharya³

et al. 2001

Acta Crystallogr D Biol Cryst

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Repeat units based on the telomeric sequence of the ciliated protozoan Tetrahymena, d(C4A2)2, have been crystallized. Cytosine‐rich DNA stretches are known to reside in telomeres and centromeres of eukaryotic chromosomes, playing crucial roles in the structural stability of the chromosome in addition to their connection with cancer and aging. Preliminary investigations on the telomeric repeat sequence C4A2C4A2 from CD studies and X‐ray crystal data suggest it to be a right‐handed interdigitated tetraplex structure with hemiprotonated C·C+ base pairs. The molecules appear to be packed one on top of another forming a discontinuous helix along c simulating a poly‐C fibre, an arrangement which maximizes the number of cytosines stacked.

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Section: Resultsmentioning

confidence: 99%

Crystallization and preliminary investigations on a telomeric repeat sequence C₄A₂C₄A₂

Savitha

Leonidas²,

Acharya³

et al. 2001

Acta Crystallogr D Biol Cryst

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“…DNA generally forms helical structures of the B-form (or, occasionally, the A-form or Z-form), while RNA molecules are primarily built from combinations of A-form helices (Scott, 2012). All of these motifs have a well known conserved geometry, so that (with some exceptions) their secondary structure can be predicted with a higher degree of confidence than protein secondary structure (Baikalov & Dickerson, 1998). The high internal symmetry of nucleic acid helices adds nontrivial complications to the MR search functions (Baikalov & Dickerson, 1998).…”

Section: Properties Of Nucleic Acidsmentioning

confidence: 99%

“…All of these motifs have a well known conserved geometry, so that (with some exceptions) their secondary structure can be predicted with a higher degree of confidence than protein secondary structure (Baikalov & Dickerson, 1998). The high internal symmetry of nucleic acid helices adds nontrivial complications to the MR search functions (Baikalov & Dickerson, 1998). However, in some cases, such symmetry may constitute an advantage for the MR approach by allowing structure solution even in the absence of experimental models (see below).…”

Section: Properties Of Nucleic Acidsmentioning

confidence: 99%

“…As a result, small changes in solvent molecules can cause very pronounced non-isomorphism in nucleic acid structures. This non-isomorphism can lead to difficulties in MR and similarly affects heavy-atom replacement techniques such as single/multiple isomorphous replacement (SIR/MIR; Baikalov & Dickerson, 1998).…”

Section: Isomorphism Of Nucleic Acid Structuresmentioning

confidence: 99%

“…Moreover, the vast majority of software currently used for data analysis and structure determination can process nucleic acid structures as efficiently as protein structures. However, in comparison to protein crystallography, nucleic acid crystallography does present certain technical and practical challenges (Baikalov & Dickerson, 1998). These differences strongly affect the choice and the design of MR search models, which is the most crucial step in obtaining correct structure solutions (Evans & McCoy, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Solving nucleic acid structures by molecular replacement: examples from group II intron studies

Marcia

Narayanan

Keating

et al. 2013

Acta Crystallogr D Biol Cryst

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Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecularreplacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecularreplacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

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Crystallographic study on oligonucleotide coiled-coils

Luchi

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En la presente tesis doctoral se han realizado estudios estructurales de DNA. Estudios previos han demostrado que los coiled-coils de d(ATATATATATAT) y d(ATATATATAT) tienen unos parámetros geométricos muy diferentes. El objetivo de esta tesis es aclarar las propiedades de los coiled-coils. Con esta finalidad se han estudiado por cristalografía de Rayos X oligonucleótidos con diferentes secuencias y con extremos cohesivos que fijen la geometría de los coiled-coils. Se han utilizado oligonucleótidos con la secuencia d(CG)n(AT)m o (AT)m(CG)n y otros semejantes. En la mayor parte de ellos n=1 y m>1, con lo que el extremo cohesivo es normalmente la secuencia CG. La estructura (a una resolución de 3.1 Å) de los cristales generados por la secuencia d(CGATATATATAT) ha sido resuelta y publicada (De Luchi et al., ChemBiochem 2006, 7, 585-587). La estructura es isomorfa con la estructura de d(AT)6 y los enlaces a puente de hidrogeno entre las bases A y T son de tipo Hoogsteen, como en el caso de la secuencia d(ATATAT). Se han obtenido diferentes tipos de coiled-coils y se han estudiado sus características y propiedades. Hemos analizado las propiedades geométricas de los coiled coils: hemos visto que los parámetros que determinan el numero de oligonucleótidos por vuelta son el "kink angle" θ, y el ángulo de torsión τ. Ha sido estudiada la relación entre estos parámetro, en función del numero de oligonucleótidos por vuelta N y el ángulo de inclinación β del coiled-coil. Hemos intentado determinar si la formación de apareamientos de tipo Hoogsteen puede influir en la geometría de los coiled-coils, los resultados sugieren que los puentes de hidrogeno de tipo Hoosteeen favorecen la formación de coiled-coils, mientras los enlaces de tipo Watson-Crick generan mas fácilmente estructuras estándar de DNA pseudocontinuas. La secuencia d(CGATATGCATAT) genera columnas tradicionales de DNA, las bases centrales G y C, apareándose con enlaces Watson-Crick fuerzan las bases ATs a aparearse de la misma manera, generando así una hélice recta pseudocontinua. Como complemento de estos estudios se han obtenido las curvas de fusión de oligonucleótidos ricos en AT, los resultados, que incluyen una formula que permite un calculo aproximado de la temperatura de fusión de secuencias cortas de DNA, han sido publicados (De Luchi et al., Analytical Biochemistry, 2003, 322, 279-282). También he tenido la oportunidad de refinar la estructura de d(TAGG) en complejo con un derivado antraquinonico que ya había sido resuelta en nuestro laboratorio. Inesperadamente, encontramos que en esta estructura no se forman G-cuádruplex como fue descrito en solución por Kettani et al, las moléculas de fármaco, a través de interacciones de stacking forman un retículo de columnas perpendiculares una a la otra, estabilizado en los "crossing points" por las flexibles y cortas moléculas de DNA. La flexibilidad del DNA gracias a sus siete ángulos de torsión, le permite adoptar una conformación tal que se adapta a la estructura creada por las columnas de fármaco. La capacidad de formar diferentes tipos de enlaces a puente de hidrogeno estabiliza su conformación en este caso no canónica. En esta estructura hemos encontrado los siguientes tipos de enlaces a puente de hidrogeno: estándar Watson-Crick, reverse Watson-Crick, interacciones simétricas Guanina-Guanina.

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Molecular Replacement Using DNA Helical Symmetry

Cited by 3 publications

References 18 publications

Crystallization and preliminary investigations on a telomeric repeat sequence C₄A₂C₄A₂

Crystallization and preliminary investigations on a telomeric repeat sequence C₄A₂C₄A₂

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

Crystallographic study on oligonucleotide coiled-coils

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Molecular Replacement Using DNA Helical Symmetry

Cited by 3 publications

References 18 publications

Crystallization and preliminary investigations on a telomeric repeat sequence C4A2C4A2

Crystallization and preliminary investigations on a telomeric repeat sequence C4A2C4A2

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

Crystallographic study on oligonucleotide coiled-coils

Contact Info

Product

Resources

About

Crystallization and preliminary investigations on a telomeric repeat sequence C₄A₂C₄A₂

Crystallization and preliminary investigations on a telomeric repeat sequence C₄A₂C₄A₂