Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

Abrescia, Nicola G. A.; Thompson, Andrew; Huynh‐Dinh, Tam; Subirana, Juan A.

doi:10.1073/pnas.052675499

Cited by 95 publications

(108 citation statements)

References 37 publications

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“…The structure obtained shows the same essential features as the structure previously found in the P2 1 space group (Abrescia et al, 2002). The bases are paired according to the Hoogsteen scheme.…”

Section: Structure Refinementsupporting

confidence: 66%

“…Once the structure of d(ApTpApTpApT) in the space group P2 1 was solved showing the presence of Hoogsteen base pairs (Abrescia et al, 2002), it became clear that the standard B-DNA models previously employed were not suitable for molecular replacement in the hexagonal case. Thus, using this new DNA as a search model form and with the information of possible twinning, we repeated the phasing via molecular replacement in the space group P6 5 .…”

Section: Molecular Replacement and Space-group Assignmentmentioning

confidence: 99%

“…We subsequently obtained crystals in the P2 1 space group. Only when the latter structure was solved by the MAD method (Abrescia et al, 2002) were we able to ®nalize the study of the d(ApTpApTpApT) crystals in the hexagonal lattice as described in this paper.…”

Section: Introductionmentioning

confidence: 99%

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When pseudosymmetry and merohedral twinning come across: the case of the d(ApTpApTpApT) oligonucleotide in a hexagonal lattice

Abrescia¹,

Subirana²

2002

Acta Crystallogr D Biol Cryst

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The d(ApTpApTpApT) deoxyhexanucleotide packs in two different lattice systems: monoclinic and hexagonal. In this study, it is shown that in the hexagonal crystals twinning and pseudosymmetry coexist. The presence of both components resulted in a puzzling space‐group determination. Only when a correct model became available [Hoogsteen‐DNA; Abrescia et al. (2002), Proc. Natl Acad. Sci. USA, 99, 2806–2811] was it possible to discriminate between twinning and pseudosymmetry. Here, the steps that led to a correct space‐group assignment and to the solution of the oligonucleotide structure in the hexagonal lattice by molecular replacement are described.

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Section: Structure Refinementsupporting

confidence: 66%

Section: Molecular Replacement and Space-group Assignmentmentioning

confidence: 99%

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When pseudosymmetry and merohedral twinning come across: the case of the d(ApTpApTpApT) oligonucleotide in a hexagonal lattice

Abrescia¹,

Subirana²

2002

Acta Crystallogr D Biol Cryst

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“…Due to their intrinsic palindromic sequence they may form cruciform structures. At the base pairing level, they may show both 4 standard Watson Crick and Hoogsteen forms [2,3]. Mixed structures with both pairing systems have been recently described [4].…”

Section: Unique Structural Properties Of Alternating At Sequencesmentioning

confidence: 99%

The distribution of alternating AT sequences in eukaryotic genomes suggests a role in homologous chromosome recognition in meiosis

Subirana

Messeguer

2011

Journal of Theoretical Biology

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There are general features of chromosome dynamics, such as homologue recognition in early meiosis, which are expected to involve related sequence motifs in non-coding DNA, with a similar distribution in different species. A search for such motifs is presented here. It has been carried out with the CONREPP program. It has been found that short alternating AT sequences (10-20 bases) have a similar distribution in most eukaryotic organisms, with some exceptions related to unique meiotic features. All other microsatellite and repeat sequences vary significantly in different organisms. It is concluded that the unique structural features and uniform distribution of alternating AT sequences indicate that they may facilitate homologous chromosome pairing in the early preleptotene stage of meiosis. They may also play a role in the compaction of DNA in mitotic chromosomes.

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“…[22] They called that structure X-DNA and suggested that this X-DNA is a right handed anti-parallel double helix with Hoogsteen base-pairs that were found by Abrescia et al some years ago. [21,23] In this Hoogsteen DNA [23] the overall helical parameters are similar to that of B-DNA with the adenines in syn-conformation. Therefore one hypothesis is that the fully modified iso-bicyclo-AT duplex S6:S7 forms such an X-DNA structure.…”

Section: Discussionmentioning

confidence: 69%

Synthesis and Properties of Isobicyclo‐DNA

Gerber

Leumann

2013

Chemistry A European J

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Abstract:We present the synthesis of the iso-bicyclo DNA building blocks with the nucleobases A, C, G and T, as well as biophysical and biological properties of oligonucleotides derived thereof. The synthesis of the sugar part was achieved in 5 steps starting from a known intermediate of the tricyclo-DNA synthesis. Dodecamers containing single iso-bicyclo thymidine incorporations, fully modified A-and T-containing sequences and fully modified oligonucleotides containing all four bases were synthesized and characterized. Iso-bicyclo DNA forms stable duplexes with natural nucleic acids with a pronounced preference for DNA over RNA as complements. The most stable duplexes, however, arise by self-pairing. Iso-bicyclo DNA forms preferentially B-DNA-like duplexes with DNA and A-like duplexes with complementary RNA as determined by CD-spectroscopy. Self-paired duplexesshow a yet unknown structure, as judged from CD-spectroscopy. Biochemical tests revealed that isobicyclo DNA is stable in fetal bovine serum and does not elicit RNase H activity.

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Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

Cited by 95 publications

References 37 publications

When pseudosymmetry and merohedral twinning come across: the case of the d(ApTpApTpApT) oligonucleotide in a hexagonal lattice

When pseudosymmetry and merohedral twinning come across: the case of the d(ApTpApTpApT) oligonucleotide in a hexagonal lattice

The distribution of alternating AT sequences in eukaryotic genomes suggests a role in homologous chromosome recognition in meiosis

Synthesis and Properties of Isobicyclo‐DNA

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