A host–guest approach for determining drug–DNA interactions: an example using netropsin

Netropsin is a well-characterized DNA minor groove binding compound that serves as a model for the study of drug–DNA interactions. Our laboratory has developed a novel host–guest approach to study drug–DNA interactions in which the host, the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) is co-crystallized with a DNA oligonucleotide guest in the presence and absence of drug. We have co-crystallized netropsin with the RT fragment bound to the symmetric 16mer d(CTTAATTCGAATTAAG)(2) and determined the structure of the complex at 1.85 Å. In contrast to previously reported netropsin–DNA structures, our oligonucleotide contains two AATT sites that bind netropsin with flanking 5′ and 3′ sequences that are not symmetric. The asymmetric unit of the RT fragment–DNA–netropsin crystals contains one protein molecule and one-half of the 16mer with one netropsin molecule bound. The guanidinium moiety of netropsin binds in a narrow part of the minor groove, while the amidinium is bound in the widest region within the site. We compare this structure to other Class I netropsin–DNA structures and find that the asymmetry of minor groove widths in the AATT site contributes to the orientation of netropsin within the groove while hydrogen bonding patterns vary in the different structures

Reply to Bhowmik et al.: Democratic climate action and studying extreme climate risks are not in tension

[no abstract available

Reply to Ruhl and Craig: Assessing and governing extreme climate risks needs to be legitimate and democratic

[No abstract available

A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a “Highly Twisted” Benzimidazole-Diamidine

A general strategy for the rapid structural analysis of DNA binding ligands is described as it was applied to the study of RT29, a new benzimidazole-diamidine compound containing a highly twisted diphenyl ether linkage. By combining the existing high-throughput fluorescent intercalator displacement (HT-FID) assay developed by Boger et al. and a high-resolution (HR) host-guest crystallographic technique, a system was produced that was capable of determining detailed structural information pertaining to RT29-DNA interactions within ~ 3 days. Our application of the HT-HR strategy immediately revealed that RT29 has a preference for four-base pair, A/T-rich sites (AATT) and a similar tolerance and affinity for three A·T-base pair sites (such as ATTC) containing a G·C base pair. Based on these selectivities, oligonucleotides were designed and the host-guest crystallographic method was used to generate diffraction quality crystals. Analysis of the resulting crystal structures revealed that the diphenyl ether moiety of RT29 undergoes conformational changes that allow it to adopt a crescent shape that now complements the minor groove structure. The presence of a G·C base pair in the RT29 binding site of ATTC did not overly perturb its interaction with DNA - the compound adjusted to the nucleobases that were available through water-mediated interactions. Our analyses suggest that the HT-HR strategy may be used to expedite the screening of novel minor groove binding compounds leading to a direct, HR structural determination

The many possible climates from the Paris Agreement’s aim of 1.5 °C warming

The United Nations’ Paris Agreement includes the aim of pursuing efforts to limit global warming to only 1.5 °C above pre-industrial levels. However, it is not clear what the resulting climate would look like across the globe and over time. Here we show that trajectories towards a ‘1.5 °C warmer world’ may result in vastly different outcomes at regional scales, owing to variations in the pace and location of climate change and their interactions with society’s mitigation, adaptation and vulnerabilities to climate change. Pursuing policies that are considered to be consistent with the 1.5 °C aim will not completely remove the risk of global temperatures being much higher or of some regional extremes reaching dangerous levels for ecosystems and societies over the coming decades

() Minor groove widths of DNA base-pair steps (from 3DNA calculations) in the absence (open circle) and presence (black diamond) of netropsin

<p><b>Copyright information:</b></p><p>Taken from "A host–guest approach for determining drug–DNA interactions: an example using netropsin"</p><p>Nucleic Acids Research 2005;33(13):4106-4116.</p><p>Published online 27 Jul 2005</p><p>PMCID:PMC1181240.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> () Stereo diagram of structures of DNA in the absence (red) and presence (blue) of netropsin (r.m.s.d = 0.9 Å). Superimpositioning of C1′ of all 16 bp was done using O ()

() The initial 2– map of the netropsin density contoured at 1σ is shown in a green cage rendering with the final netropsin model superimposed in magenta

<p><b>Copyright information:</b></p><p>Taken from "A host–guest approach for determining drug–DNA interactions: an example using netropsin"</p><p>Nucleic Acids Research 2005;33(13):4106-4116.</p><p>Published online 27 Jul 2005</p><p>PMCID:PMC1181240.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> () The final 2– map of netropsin density contoured at 1σ is shown also in a green cage rendering with the final refined model of netropsin superimposed in magenta. () The final 2– map is shown superimposed on the final DNA model in blue sticks and the final netropsin model in a magenta ball-and-stick rendering