Glucose-Nucleobase Pseudo Base Pairs: Biomolecular Interactions within DNA

Noncovalent forces rule the interactions between biomolecules. Inspired by a biomolecular interaction found in aminoglycoside-RNA recognition, glucose-nucleobase pairs have been examined. Deoxyoligonucleotides with a 6-deoxyglucose insertion are able to hybridize with their complementary strand, thus exhibiting a preference for purine nucleobases. Although the resulting double helices are less stable than natural ones, they present only minor local distortions. 6-Deoxyglucose stays fully integrated in the double helix and its OH groups form two hydrogen bonds with the opposing guanine. This 6-deoxyglucose-guanine pair closely resembles a purine-pyrimidine geometry. Quantum chemical calculations indicate that glucose-purine pairs are as stable as a natural T-A pair. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.We thank the Ministerio de Economía y Competitividad (CTQ2011- 15203-E, CTQ2012-35360, CTQ2014-52588-R, BFU2014-52864-R), the Netherlands Organization for Scientific Research (NWO-CW and NWO-EW), and the National Research School Combination—Catalysis (NRSC-C) for financial support. E.V.C. thanks Ministerio de Educación, Cultura y Deporte for a FPU fellowship and Cost Action CM1005 for a STSM grant.Peer reviewe

Synthesis and Biophysical Investigations of Oligonucleotides Containing Galactose-Modified DNA, LNA and 2'-Amino-LNA Monomers

Galactose-modified thymidine, LNA-T, and 2′-amino-LNA-T nucleosides were synthesized, converted into the corresponding phosphoramidite derivatives and introduced into short oligonucleotides. Compared to the unmodified control strands, the galactose-modified oligonucleotides in general, and the N2′-functionalized 2′-amino-LNA derivatives in particular, showed improved duplex thermal stability against DNA and RNA complements and increased ability to discriminate mismatches. In addition, the 2′-amino-LNA-T derivatives induced remarkable 3′-exonuclease resistance. These results were further investigated using molecular modeling studies.Foundation VILLUM; BIONEC (VKR022710); Ministerio de Economía y Competitividad (CTQ-2012-35360); German Research Foundation (DFG

Glucose-nucleobase pairs within DNA: impact of hydrophobicity, alternative linking unit and DNA polymerase nucleotide insertion studies

Recently, we studied glucose-nucleobase pairs, a binding motif found in aminoglycoside–RNA recognition. DNA duplexes with glucose as a nucleobase were able to hybridize and were selective for purines. They were less stable than natural DNA but still fit well on regular B-DNA. These results opened up the possible use of glucose as a non-aromatic DNA base mimic. Here, we have studied the incorporation and thermal stability of glucose with different types of anchoring units and alternative apolar sugar-nucleobase pairs. When we explored butanetriol instead of glycerol as a wider anchoring unit, we did not gain duplex thermal stability. This result confirmed the necessity of a more conformationally restricted linker to increase the overall duplex stability. Permethylated glucose-nucleobase pairs showed similar stability to glucoside-nucleobase pairs but no selectivity for a specific nucleobase, possibly due to the absence of hydrogen bonds between them. The three-dimensional structure of the duplex solved by NMR located both, the hydrophobic permethylated glucose and the nucleobase, inside the DNA helix as in the case of glucose-nucleobase pairs. Quantum chemical calculations on glucose-nucleobase pairs indicate that the attachment of the sugar to the DNA skeleton through the OH1 or OH4 positions yields the highest binding energies. Moreover, glucose was very selective for guanine when attached through OH1 or OH4 to the DNA. Finally, we examined DNA polymerase insertion of nucleotides in front of the saccharide unit. KF− polymerase from E. coli inserted A and G opposite glc and 6dglc with low efficiency but notable selectivity. It is even capable of extending the new pair although its efficiency depended on the DNA sequence. In contrast, Bst 2.0, SIII and BIOTAQ™ DNA polymerases seem to display a loop-out mechanism possibly due to the flexible glycerol linker used instead of deoxyribose.We thank the Ministerio de Economia y Competitividad (CTQ2011-15203-E, CTQ2012-35360, CTQ2014-52588-R, CTQ2015- 64275-P, BFU2014-52864-R, and BFU2017-89707-P) and the Netherlands Organization for Scientific Research (NWO-CW and NWO-EW) for financial support. E. V. C. thanks the Ministerio de Educación, Cultura y Deporte for an FPU fellowship and Cost Action CM1005 for an STSM grant. R. L. is a recipient of a Talent Hub fellowship from Junta de AndaluciaPeer reviewe

Targeted siRNA Delivery Using Lipid Nanoparticles

Efficient intracellular delivery of small-interfering ribonucleic acid (siRNA) to the target organ or tissues in the body is assumed as the main hurdle for a widespread use of siRNAs in the clinics. Solid lipid-based nanoparticles (SLNs) and derivatives can potentially fit this purpose by enabling to overcome the extracellular and intracellular physiological barriers affecting the delivery. For that, rational formulations and rational process designs are needed. This chapter addresses a comprehensive description and critical appraisal of the main production methods of this particular type of lipid nanoparticles and the leading strategies to prompt a targeted delivery of siRNA