DNA-NH<sub>2</sub> acylation reaction: Molecular weight or conformation dominates?

Abstract

DNA has the unique chemical and physical characteristics as a carrier of genetic information. With the development of structural DNA nanotechnology, it has been recognized that DNA can perform versatile functions with promising applications in nanomachine, computing, sensing and nanoarchitectures. In addition, the chemical incorporation with various functional groups brings in a diverse range of additional properties to DNA molecules for broadened applications. Therefore, post-synthetic modification of DNA has been widely used to introduce additional functionalities to DNA molecules, for example, design and synthesis of DNA-encoded library, preparation of DNA-based probes for biosensing, improving binding activities of DNA aptamers, etc. The modification efficiency is determined by both the intrinsic factors of the molecules involved (DNA and reagents) and the external factors (experimental conditions). However, previous studies on the modification focused on the optimization of reaction conditions. To determine the important intrinsic factors that affect modification efficiency, we have conducted a systematic study on the reaction with a model system— acylation of amino-DNA. Nine amino-modified DNAs with two different DNA conformations (a–i) were reacted with two carboxylic acids with different molecule weights (12-oxo-2,5,8,11-tetraoxapentadecan-15-oic acid, M W 264.1209, and 30-oxo-2,5,8,11,14,17,20,23,26,29-decaoxatritriacontan-33-oic acid, M W 528.2782), respectively, and characterized by polyacrylamide gel electrophoresis (PAGE). The bands were analyzed and calculated by Image J . In the present study, three factors are considered for the design. First, acylation is one of the most widely methods used for chemical modifications of DNA. The acylation reactions afford amides and these amides binding to DNA form more structurally complex and diverse DNA building blocks. Therefore, we explored the acylation reaction between amino-modified DNA with carboxylic acids. Second, two DNA conformations (single-stranded random coils, ssDNAs, and rigid, double-stranded DNA duplexes, dsDNA) were included. Single-stranded DNAs are more flexible than rigid DNA duplexes and thus can provide more variability in terms of modulating orientation of the reaction group to facilitate reactions. Third, the two small organic molecules with a varying number of polyethylene glycol (PEG) units were used, because PEG has been widely used in the field of chemical modification of biomacromolecules due to its excellent properties including a wide range of solubility, predominant bio-compatibility, good stability, low toxicity and no irritation, etc. We, therefore, systematically studied the DNA modification reaction to investigate the influences of two intrinsic factors ( M W and conformation) on the reaction. The primary factor for DNA-NH2 acylation reaction is molecular weight ( M W). The higher the M W of the regents (both small molecules and DNAs) are, the slower the reactions are. DNA conformation plays a much minor role in the reaction. Compared with rigid dsDNA duplexes, flexible ssDNA chains facilitate reactions. Based on the current study, we would suggest for post-synthetic modification of DNA: (1) Keep the molecular weights of all reagents (both small molecules and DNA molecules) to the minimal in the design to allow fast diffusion. (2) Keep the DNA strands near the modification location to be single stranded to facilitate orientation adjustment. If high molecular weight and rigid conformation (duplex) are not avoidable, reaction time and/or reagent concentration should be elongated to ensure the modification efficiency.