A C-14 labeled Py–Im polyamide localizes to a subcutaneous prostate cancer tumor

AbstractIn an effort to quantitate Py–Im polyamide concentrations in vivo, we synthesized the C-14 radioactively labeled compounds 1–3, and investigated their tumor localization in a subcutaneous xenograft model of prostate cancer (LNCaP). Tumor concentrations were compared with representative host tissues, and exhibited a certain degree of preferential localization to the xenograft. Compound accumulation upon repeated administration was measured. Py–Im polyamide 1 was found to accumulate in LNCaP tumors at concentrations similar to the IC50 value for this compound in cell culture experiments

Synthesis of Cyclic Py-Im Polyamide Libraries

Cyclic Py-Im polyamides containing two GABA turn units exhibit enhanced DNA binding affinity, but extensive studies of their biological properties have been hindered due to synthetic inaccessibility. A facile modular approach toward cyclic polyamides has been developed via microwave-assisted solid-phase synthesis of hairpin amino acid oligomer intermediates followed by macrocyclization. A focused library of cyclic polyamides 1–7 targeted to the androgen response element (ARE) and the estrogen response element (ERE) were synthesized in 12–17% overall yield. The Fmoc protection strategy also allows for selective modifications on the GABA turn units that have been shown to improve cellular uptake properties. The DNA binding affinities of a library of cyclic polyamides were measured by DNA thermal denaturation assays and compared to the corresponding hairpin polyamides. Fluorescein-labeled cyclic polyamides have been synthesized and imaged via confocal microscopy in A549 and T47D cell lines. The IC_50 values of compounds 1–7 and 9–11 were determined, revealing remarkably varying levels of cytotoxicity

Role of Mismatch Repair Enzymes in GAA•TTC Triplet-repeat Expansion in Friedreich Ataxia Induced Pluripotent Stem Cells

The genetic mutation in Friedreich ataxia (FRDA) is a hyperexpansion of the triplet-repeat sequence GAA•TTC within the first intron of the FXN gene. Although yeast and reporter construct models for GAA•TTC triplet-repeat expansion have been reported, studies on FRDA pathogenesis and therapeutic development are limited by the availability of an appropriate cell model in which to study the mechanism of instability of the GAA•TTC triplet repeats in the human genome. Herein, induced pluripotent stem cells (iPSCs) were generated from FRDA patient fibroblasts after transduction with the four transcription factors Oct4, Sox2, Klf4, and c-Myc. These cells were differentiated into neurospheres and neuronal precursors in vitro, providing a valuable cell model for FRDA. During propagation of the iPSCs, GAA•TTC triplet repeats expanded at a rate of about two GAA•TTC triplet repeats/replication. However, GAA•TTC triplet repeats were stable in FRDA fibroblasts and neuronal stem cells. The mismatch repair enzymes MSH2, MSH3, and MSH6, implicated in repeat instability in other triplet-repeat diseases, were highly expressed in pluripotent stem cells compared with fibroblasts and neuronal stem cells and occupied FXN intron 1. In addition, shRNA silencing of MSH2 and MSH6 impeded GAA•TTC triplet-repeat expansion. A specific pyrrole-imidazole polyamide targeting GAA•TTC triplet-repeat DNA partially blocked repeat expansion by displacing MSH2 from FXN intron 1 in FRDA iPSCs. These studies suggest that in FRDA, GAA•TTC triplet-repeat instability occurs in embryonic cells and involves the highly active mismatch repair system

Quantitative microarray profiling of DNA-binding molecules

A high-throughput Cognate Site Identity (CSI) microarray platform interrogating all 524 800 10-base pair variable sites is correlated to quantitative DNase I footprinting data of DNA binding pyrrole-imidazole polyamides. An eight-ring hairpin polyamide programmed to target the 5 bp sequence 5'-TACGT-3' within the hypoxia response element (HRE) yielded a CSI microarray-derived sequence motif of 5'-WWACGT-3' (W = A,T). A linear beta-linked polyamide programmed to target a (GAA)_3 repeat yielded a CSI microarray-derived sequence motif of 5'-AARAARWWG-3' (R = G,A). Quantitative DNase I footprinting of selected sequences from each microarray experiment enabled quantitative prediction of K_a values across the microarray intensity spectrum

Quantitative microarray profiling of DNA-binding molecules

A high-throughput Cognate Site Identity (CSI) microarray platform interrogating all 524 800 10-base pair variable sites is correlated to quantitative DNase I footprinting data of DNA binding pyrrole-imidazole polyamides. An eight-ring hairpin polyamide programmed to target the 5 bp sequence 5'-TACGT-3' within the hypoxia response element (HRE) yielded a CSI microarray-derived sequence motif of 5'-WWACGT-3' (W = A,T). A linear beta-linked polyamide programmed to target a (GAA)_3 repeat yielded a CSI microarray-derived sequence motif of 5'-AARAARWWG-3' (R = G,A). Quantitative DNase I footprinting of selected sequences from each microarray experiment enabled quantitative prediction of K_a values across the microarray intensity spectrum

Stalled DNA Replication Forks at the Endogenous GAA Repeats Drive Repeat Expansion in Friedreich’s Ataxia Cells

Friedreich’s ataxia (FRDA) is caused by the expansion of GAA repeats located in the Frataxin (FXN) gene. The GAA repeats continue to expand in FRDA patients, aggravating symptoms and contributing to disease progression. The mechanism leading to repeat expansion and decreased FXN transcription remains unclear. Using single-molecule analysis of replicated DNA, we detected that expanded GAA repeats present a substantial obstacle for the replication machinery at the FXN locus in FRDA cells. Furthermore, aberrant origin activation and lack of a proper stress response to rescue the stalled forks in FRDA cells cause an increase in 3′-5′ progressing forks, which could enhance repeat expansion and hinder FXN transcription by head-on collision with RNA polymerases. Treatment of FRDA cells with GAA-specific polyamides rescues DNA replication fork stalling and alleviates expansion of the GAA repeats, implicating DNA triplexes as a replication impediment and suggesting that fork stalling might be a therapeutic target for FRDA

Understanding Microbialite Morphology Using a Comprehensive Suite of Three-Dimensional Analysis Tools

Abstract Microbialites can have complex morphologies that preserve clues to ancient microbial ecology. However, extracting and interpreting these clues is challenging due to both the complexity of microbial structures and the difficulties of connecting morphology to microbial processes. Fenestrate microbialites from the 2521 -3 Ma Gamohaan Formation, South Africa, have intricate structures composed of three distinct microbial structures: steeply dipping supports (surfaces defined by organic inclusions), more shallowly dipping supports with diffuse organic inclusions below them, and draping laminae. In polished slabs, shallowly dipping supports with diffuse organic inclusions show apparent dips from 27°to 60°, and supports without associated zones of diffuse inclusions dip 75°to 88°, which suggests a distinction between support types based on orientation. However, dips exposed in polished slabs are apparent dips, and three-dimensional analysis is required for analysis of true dips. Through the Keck Center for Active Visualization in Earth Sciences (KeckCAVES), we used locally developed software that controls a three-dimensional environment with head and hand tracking (an ''immersive environment'') to visualize and interpret virtual microbialite data sets. Immersive environments have not penetrated into standard scientific work processes (''workflows'') due to their high costs, steep learning curves, and low productivity for users. By contrast, our suite of software tools allowed us to develop a personalized scientific workflow that provides a complete path from initial ideas to characterization of fenestrate microbialites' features. Results of three-dimensional analysis of fenestrate microbialites show that supports with inclusions dip 65°to 75°, whereas supports without inclusions dip 85°to 90°. These results demonstrate that all supports have very steep dips, and a 10°dip gap exists between supports with and without inclusions, which suggests they grew in fundamentally different ways. Results also emphasize how valuable three-dimensional analysis is when combined with a comprehensive workflow for understanding intricate structures such as fenestrate microbialites

Microwave Assisted Synthesis of Py-Im Polyamides

Microwave synthesis was utilized to rapidly build Py-Im polyamides in high yields and purity using Boc-protection chemistry on Kaiser oxime resin. A representative polyamide targeting the 5′-WGWWCW-3′ (W = A or T) subset of the consensus Androgen and Glucocorticoid Response Elements was synthesized in 56% yield after 20 linear steps and HPLC purification. It was confirmed by Mosher amide derivatization of the polyamide that a chiral α-amino acid does not racemize after several additional coupling steps

Completion of a Programmable DNA-Binding Small Molecule Library

Hairpin pyrrole-imidazole (Py-Im) polyamides are programmable oligomers that bind the DNA minor groove in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. These cell-permeable small molecules have been shown to enter the nuclei of live cells and downregulate endogenous gene expression. We complete here a library of 27 hairpin Py-Im polyamides, which bind seven-base-pair sequences of the general form 5′-WWGNNNW-3′ (where W=A or T, N=W, G, or C). Their equilibrium association constants (K_a) range from K_a=1×10^8 to 4×10^(10) M^(−1) with good sequence specificity. A table of binding affinities and sequence contexts for this completed 27-member library has been assembled for the benefit of the chemical biology community interested in molecular control of transcription