Ferrocene-Linked Thymine/Uracil Conjugates: Base Pairing Directed Self-Assembly and Supramolecular Packing

Synthesis and biochemical evaluation of Aminopropanolyl-Thymine tri-Phosphate (ap-TTP)

Deoxyribonucleoside triphosphates (dNTPs) are building blocks for the biosynthesis of DNA. Various modified dNTPs' analogs have synthesized by structural changes of nucleoside's susgar and nucleobases and employed for synthesis of modified DNA. A very few modified dNTPs have prepared from non-sugar nucleoside analogs. This report describes the synthesis of acyclic nucleoside triphosphate (NTP) analog from amino acid L-Serine as aminopropanolyl-thymine triphosphate (ap-TTP) and demonstrate its biochemical evaluation as enzymatic incorporation of ap-TTP into DNA with DNA polymerases with primer extension methods. Alanyl peptide nucleicacids (Ala-PNA) are the analogs of DNA which contains alanyl backbone. Aminopropanolyl - analogs are derivatives of alanyl back bone. Ap-TTP analog is nucleoside triphosphate analog derived from Ala-PNA. Importantly, this report also sheds light on the crystal packing arrangement of alaninyl thymine ester derivative in solid-state and reveals the formation of self-duplex assembly in anti-parallel fashion via reverse Watson-Crick hydrogen bonding and π-π interactions. Hence, ap-TTP is a useful analog which also generates the free amine functional group at the terminal of DNA oligonucleotide after incorporation.

The many facets of adenine: coordination, crystal patterns, and catalysis

Canonical purine-pyrimidine base pairs, the key to the complementary hydrogen bonding in nucleic acids, are fundamental molecular recognition motifs crucial for the formation and stability of double-helical DNA. Consequently, focused study and modeling of nucleobase hydrogen-bonding schemes have spawned a vast array of chemical and biophysical investigations. The Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen hydrogen-bonding schemes stabilize various nucleic acid structures. As a result, numerous modified bases have been designed to maximize such interactions, addressing specific problems related to base pairing and giving rise to supramolecular ensembles in solution or in the solid state. It is also important to realize that suitably predisposed imino nitrogens and other functional groups present in heterocyclic nucleobases present a versatile molecular framework for the construction of coordination architectures, which may be harnessed to mimic base polyads and higher order nucleic acid structures. Adenine, a purine nucleobase, is an important naturally occurring nitrogen heterocycle present in nucleic acids. It is notable that the adenine unit is also frequently encountered as an inextricable part of enzyme cofactors and second messenger systems, such as NAD(+), FADH(2), and cAMP, which are essential for certain catalytic reactions and biochemical processes. In addition, a crucial catalytic role of the adenine moiety is also observed in group II intron catalysis and at the ribosomal peptidyltransferase center. Such versatile functional roles of the adenine framework serve as an inspiration for addressing research problems, ranging from classical coordination chemistry to the development of new materials. In this Account, we begin by describing the emerging use of adenine nucleobase for the design of metal-nucleobase frameworks. The coordination of metal ions affords a variety of oligomeric and polymeric species; we focus on silver- and copper-based structures and also discuss ferrocenylated adenine tetrads. We then consider the use of supramolecular adenine coordination complexes for transferring molecular properties onto surfaces. This technique is particularly useful for transferring noncovalent interactions, such as van der Waals forces, electrostatic interactions, and hydrogen bonding, to designed architectures in nanoscale applications. Finally, we explore the issue of adenine-based catalytic entities. Here, adenine moieties are first fixed in a polymeric matrix, followed by metalation of the matrix. These metalated adenine-containing polymers are then assayed for catalytic assistance in various chemical and biochemical reactions. Taken together, the versatile coordination abilities and hydrogen-bonding capacity of adenine offer a novel entry point for a natural ligand into materials synthesis.