Design, Synthesis, and Hybridisation of Water‐Soluble, Peptoid Nucleic Acid Oligomers Tagged with Thymine

Abstract

The preparation of a new class of backbone-modified PNA\ud mimetic incorporating thymine is described. Target dipeptoid\ud monomer 21 was synthesised from an N-[2-(thymin-1-yl)ethyl]\ud glycinate ester and a properly protected iminodiacetic\ud acid. The distinctive structural motif in the backbone is a\ud carboxy group, inserted to impart water solubility to the\ud oligomer. Two achiral oligopeptoid sequences (8-mer and 12-\ud mer), characterised by the shift of the amide carbonyl group\ud away from the nucleobase, were efficiently assembled according\ud to solid-phase synthesis protocols. Thermal denatur-ation studies showed that the two homopyrimidine oligopeptoids\ud do not effectively hybridise with complementary sequences\ud of DNA and RNA or fully synthetic (2,4-diamino)-\ud triazin-6-yl-tagged peptoid 22. A possible reason could reside\ud in the concurrent unfavourable influence of the anionic\ud N-(carboxymethyl) moieties and the flexible nucleobase/\ud backbone ethylene linker

Efficient Method for the Concentration Determination of Fmoc Groups Incorporated in the Core-Shell Materials by Fmoc–Glycine

“…The similar value was also used for DMF solution: ε (266 nm) = 17,500 dm 3 × mol −1 × cm −1 , ε (289 nm) = 5800 dm 3 × mol −1 × cm −1 and ε (300 nm) 7800 dm 3 × mol −1 × cm −1 [ 71 ]. In many studies only one ε coefficient (301 nm) 7800 dm 3 × mol −1 × cm −1 was used for the calculation of the loading of amino acids and other molecules on a resin [ 69 , 72 , 73 , 74 , 75 ].…”

Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure

“…It is also interesting to mention that, on the other hand, negatively charged nucleopeptoids carrying a poly(dT) sequence were not able to hybridize both poly(dA) and poly(rA). This proved that electrostatic interactions associated with adequate flexibility and three-dimensional presentation of the functional groups of the backbone provide determinant contributions for efficient RNA recognition [ 59 ]. Besides the RNA binding ability, many other interesting properties of the nucleobase-containing peptide-like molecules are known in the field of biomedicine, including the antigene activity and the modulation of the expression and function of noncoding RNAs [ 60 – 61 ].…”

Synthesis of a thymine-functionalized nucleoamino acid for the solid phase assembly of cationic nucleopeptides

“…In several research studies, it has been shown that various modifications of sugar phosphodiester linkage of nucleic acids can lead to oligonucleotide analogs with useful properties (Abramova et al 1991;Bell and Micklefield 2009;D'Alonzo et al 2011;D'Onofrio et al 2005;Zarra et al 2009;Zatsepin et al 2003). Interestingly, an extensive research work was conducted by many researchers on peptide-based analogs of nucleic acids (also referred to as nucleopeptides) which in some cases were characterized by a good intrinsic cell-membrane permeability as well as a significant ability to interact with natural nucleic acids leading to complexes of high thermal stability (Roviello et al 2010a).…”