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Polyglutamine repeats in proteins are highly correlated with amyloid formation and neurological disease. To better understand the molecular basis of glutamine repeat diseases, structural analysis of polyglutamine peptides as soluble monomers, oligomers, and insoluble amyloid fibrils is necessary. In this study, fluorescence resonance energy transfer (FRET) experiments and molecular dynamics simulations using different theoretical models of polyglutamine were conducted. This study demonstrates that a previously proposed simple CαCβ model of polyglutamine, denoted as FCO, accurately reproduced the present FRET results and the results of previously published FRET, triplet-state quenching, and fluorescence correlation studies. Other simple CαCβ models with random coil and extended β-strand parameters, and all-atom models with parm96 and parm99SB force fields, did not match the FRET result well. The FCO is an intrinsically disordered model with a high-effective persistence length producing extended peptides at short lengths (QN 16. Proteins 2011. © 2010 Wiley-Liss, Inc.

Sonogashira coupling of diacetyl 5-ethynyl-2′-deoxyuridine with diacetyl 5-iodo-2′-deoxyuridine gave the acylated ethynediyl-linked 2′-deoxyuridine dimer (3 b; 63 %), which was deprotected with ammonia/methanol to give ethynediyl-linked 2′-deoxyuridines (3 a; 79 %). Treatment of 5-ethynyl-2′-deoxyuridine (1 a) with 5-iodo-2′-deoxyuridine gave the furopyrimidine linked to 2′-deoxyuridine (78 %). Catalytic oxidative coupling of 1 a (O2, CuI, Pd/C, N,N-dimethylformamide) gave butadiynediyl-linked 2′-deoxyuridines (4; 84 %). Double Sonogashira coupling of 5-iodo-2′-deoxyuridine with 1,4-diethynylbenzene gave 1,4-phenylenediethynediyl-bridged 2′-deoxyuridines (5; 83 %). Cu-catalyzed cycloisomerization of dimers 4 and 5 gave their furopyrimidine derivatives. One-electron addition to 1 a, 3 a, and 4 gave the anion radical, the EPR spectra of which showed that the unpaired electron is largely localized at C6 of one uracil ring (17 G doublet) at 77 K. The EPR spectra of the one-electron-oxidized derivatives of ethynediyl- and butadiynediyl-linked uridines 3 a and 4 at 77 K showed that the unpaired electron is delocalized over both rings. Therefore, structures 3 a and 4 provide an efficient electronic link for hole conduction between the uracil rings. However, for the excess electron, an activation barrier prevents coupling to both rings. These dimeric structures could provide a gate that would separate hole transfer from electron transport between strands in DNA systems. In the crystal structure of acylated dimer 3 b, the bases were found in the anti position relative to each other across the ethynyl link, and similar anti conformation was preserved in the derived furopyrimidine–deoxyuridine dinucleoside.