Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex

Schneider, Christoph; Brandl, Maria T.; Sühnel, Jürgen

doi:10.1006/jmbi.2000.4338

Cited by 42 publications

(55 citation statements)

References 30 publications

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“…We have modeled it by removing the water and found that full relaxation of the model gives a proper 2-0-0-0-0-0 system with a compact structure. That the water mediated mediated system could act as a conformational switch was suggested much earlier (Schneider et al 2001). The suggestion was supported by a detailed molecular dynamics simulation study where the author could detect several cofi gurational variants of the pair including one with no water bridge.…”

Section: Multimodality In Edge Interaction Possibilities Within a Paimentioning

confidence: 72%

“…We feel that base pairs which can lend themselves easily to switch from one of the twelve geometric families (Leontis et al 2001) to another, particularly in response to subtle environmental changes could be potential candidates for acting as conformational switches. The idea is not new and molecular dynamics studies of base pairs have been carried out in order to probe into the multimodality in edge interaction possibilities within base pairs (Schneider et al 2001). A closer look at the trans G:G H:S system seemed to be important in this context.…”

Section: Multimodality In Edge Interaction Possibilities Within a Paimentioning

confidence: 99%

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Theoretical analysis of noncanonical base pairing interactions in RNA molecules

et al. 2007

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Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered for secondary structure predictions. We present results of comparative ab initio studies of stabilities and interaction energies for the three standard and 24 selected unusual RNA base pairs reported in the literature. Hydrogen added models of isolated base pairs, with heavy atoms frozen in their 'away from equilibrium' geometries, built from coordinates extracted from NDB, were geometry optimized using HF/6-31G** basis set, both before and after unfreezing the heavy atoms. Interaction energies, including BSSE and deformation energy corrections, were calculated, compared with respective single point MP2 energies, and correlated with occurrence frequencies and with types and geometries of hydrogen bonding interactions. Systems having two or more N-H...O/N hydrogen bonds had reasonable interaction energies which correlated well with respective occurrence frequencies and highlighted the possibility of some of them playing important roles in improved secondary structure prediction methods. Several of the remaining base pairs with one N-H...O/N and/or one C-H...O/N interactions respectively, had poor interaction energies and negligible occurrences. High geometry variations on optimization of some of these were suggestive of their conformational switch like characteristics.

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Section: Multimodality In Edge Interaction Possibilities Within a Paimentioning

confidence: 72%

Section: Multimodality In Edge Interaction Possibilities Within a Paimentioning

confidence: 99%

Theoretical analysis of noncanonical base pairing interactions in RNA molecules

et al. 2007

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“…Which of the postulated two geometries of the U-C pairs occurs in the RNAs: the U-Cϩ (with the neighboring carbonyl and imino groups involved in the formation of hydrogen bonds) or the neutral U-C pair (with N3-imino proton of U forming a watermediated hydrogen bond to the N3 of C)? Some answers to these questions come from the crystal structures of RNA duplexes containing the U-C pairs (43)(44)(45). It appears that the RNA duplex containing two tandem U-C mismatches in its central positions is very unstable compared with a similar duplex with the U-U mismatches (43).…”

Section: Structures Of the Sca1 Transcripts Are The Same In Cellularmentioning

confidence: 99%

“…(CAG) 45 -CAT-CAG-CAT-(CAG) 10 for which their total length (58 repeats) suggested an early onset of the disease at 22 years of age, whereas the actual age at SCA1 onset was 50 years (30). In addition, one of the SCA1 variants analyzed in this study, which belonged to an unaffected carrier, had 43 repeats in the 23-1-1-1-17 configuration (Fig.…”

Section: Structures Of the Sca1 Transcripts Are The Same In Cellularmentioning

confidence: 99%

Imperfect CAG Repeats Form Diverse Structures in SCA1 Transcripts

Sobczak

Krzyżosiak

2004

Journal of Biological Chemistry

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The expanded CAG repeat in the coding sequence of the spinocerebellar ataxia type 1 (SCA1) gene is responsible for SCA1, one of the hereditary human neurodegenerative diseases. In the normal SCA1 alleles usually 1-3 CAT triplets break the continuity of the CAG repeat tracts. Here we show what is the structural role of the CAU interruptions in the SCA1 transcripts. Depending on their number and localization within the repeat tract the interruptions either enlarge the terminal loop of the hairpin formed by the repeats, nucleate the internal loops in its stem structure, or force the repeats to fold into two smaller hairpins. Thus, the interruptions destabilize the CAG repeat hairpin, which is likely to decrease its ability to participate in the putative RNA pathogenesis mechanism driven by the long CAG repeat hairpins.

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“…MD simulations have been conducted on a r(GGACUUCGGUCC) 2 duplex that contains two G⅐U pairs framing two water-mediated C⅐U pairs. 45 It has been observed that the U⅐C pairs switch during the MD run between two types of conformations involving an interaction between the (C)NH 2 group and either the (U)O2 or the (U)O4 atoms. For the conformations involving a (C)NH 2 .…”

Section: Non-watson-crick Base Pairsmentioning

confidence: 99%