Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V

Molecular Adjuvants for DNA Vaccines: Application, Design, Preparation, and Formulation

Compared with conventional vaccines, the main advantage of DNA vaccine-based methods is its continued expression of the plasmid-encoded antigens followed by the induction of subsequent humoral and cellular immunities. DNA vaccines are currently used in animal models, but limited success has been obtained for use in clinical applications due to their poor immunogenicity. Various strategies are attempted to improve the induced immune response of DNA vaccines. It has been demonstrated that co-administration of molecular adjuvants with DNA vaccines is a promising approach to effectively elicit protective immunity by increasing the transfection efficiency of DNA vaccines. Genetic adjuvants are incorporated to promote activation of the transfected local antigen-presenting cells (APCs) and immune cells in the draining lymph node and polarization of T-cell subsets to decrease T-cell tolerance to the specific antigen. Here we provide an overview of different types of genetic adjuvants. The aim of the current chapter is to present a framework for the construction of a gene-based vaccine and adjuvant. Moreover, we describe the application of DNA vaccines co-administered with different types of genetic adjuvants and the methods to evaluate their potency in the mouse models.

In Vitro Construction of Large-scale DNA Libraries from Fragments Containing Random Regions using Deoxyinosine-containing Oligonucleotides and Endonuclease V

Efficient and precise construction of DNA libraries is a fundamental starting point for directed evolution of polypeptides. Recently, several in vitro selection methods have been reported that do not rely on cells for protein expression, where peptide libraries in the order of 10¹³ species are used for in vitro affinity selection. To maximize their potential, simple yet versatile construction of DNA libraries from several fragments containing random regions without bacterial transformation is essential. To address this issue, we herein propose a novel DNA construction methodology based on the use of polymerase chain reaction (PCR) primers containing a single deoxyinosine (I) residue near their 5' end. Treatment of the PCR products with endonuclease V generates 3' overhangs with customized lengths and sequences, which can be ligated accurately and efficiently with other fragments having exactly complementary overhangs. As a proof of concept, we constructed an artificial gene library of single-domain antibodies from four DNA fragments.

Base-Modified Nucleic Acids as a Powerful Tool for Synthetic Biology and Biotechnology

The ability of various nucleoside triphosphate analogues of deoxyguanosine and deoxycytidine with 7-deazadeoxyadenosine (A₁ ) and 5-chlorodeoxyuridine (T₁ ) to serve as substrates for Taq DNA polymerase was evaluated. The triphosphate set composed of A₁ , T₁ , and 7-deazadeoxyguanosine with either 5-methyldeoxycytidine or 5-fluorodeoxycytidine was successfully employed in the polymerase chain reaction (PCR) of 1.5 kb fragments as well as random oligonucleotide libraries. Another effective combination of triphosphates for the synthesis of a 1 kb PCR product was A₁ , T₁ , deoxyinosine, and 5-bromodeoxycytidine. In vivo experiments using an antibiotic-resistant gene containing the latter set demonstrated that the bacterial machinery accepts fully modified sequences as genetic templates. Moreover, the ability of the base-modified segments to selectively protect DNA from cleavage by restriction endonucleases was shown. This approach can be used to regulate the endonuclease cleavage pattern.