Nonenzymatic oligomerization of RNA by TNA templates, and, Isoguanine-modified thrombin aptamers, and, An antiparallel purine·purine DNA duplex, and, Synthesis and enzymatic polymerization of FNA on DNA templates, and, Thermodynamics and luminescen

Deoxyribonucleic acid encodes genetic information---transcribed into ribonucleic acid and expressed as protein after ribosomal mRNA translation. This central dogma of life has constrained the perceived repertoire of nucleic acid function to genetic expression despite coding-DNA comprising only 1.5% of the human genome. It is therefore not surprising that alternative nucleic acid functions have been found such as DNA- and RNA-enzymes, aptamers, and non-coding RNA (r, sn, mi, g, pi, p, tm, srp, and tRNA). Further, natural and modified nucleic acids are gaining favor as engineered polymers for development of nanocircuitry and architectures in addition to work exploring the origins of life.; 3'-2'-L-alpha-threose nucleic acid (TNA) is a homologue of RNA with a C5' deletion. Chimeric DNA/TNA and homo-TNA templates were found to specifically promote 5' → 3' nonenzymatic oligomerization of guanosine 5'-phosphoro-2-methylimidazole in a model prebiotic oligomerization system with efficiencies rivaling those of PNA---another candidate prebiotic nucleic acid (Chapter 1). A comprehensive library of isoguanine-substituted human alpha-thrombin-inhibiting aptamers was screened and binding affinities determined. Three aptamers with single isoguanine substitutions had stronger binding affinity than the prototype aptamer (Chapter 2). Diverging from natural purine•pyrimidine (A•T and G•C) base pairing, two complementary all-purine DNA octamers with guanine•isoguanine and diaminopurine• C7xanthine pairs were synthesized and shown to associate in a 1:1 mode. Thermodynamic stability of the artificial duplex was comparable to that calculated for the natural counterpart DNA duplex (Chapter 3). Flexible nucleic acid (FNA) is another homologue of DNA having a C2'-deletion. A novel synthesis of (R)- and (S)-fNTPs (N=A, G, C and T) was devised, and subsequent enzymatic incorporation of all fNMPs via primer-extension was shown. Apparent full-length products were observed with replacement of up to 3 fNTPs in the dNTP substrate pool using 9°Nm (9°N-7 E143D) or Therminator DNA polymerase (9°N-7 A485L exo-) (Chapter 4).; Finally, three novel DNA metallo-pairs were prepared wherein metal-coordination replaces standard Watson-Crick hydrogen bonding patterns. The metallo-pairs exhibit remarkable metal cation selectivity and duplex thermal stabilization. Additionally, the self-pair PurDP•Ln•PurDP [Ln=Eu3+ or Tb3+; PurDP=2,6-di(2'-pyridyl)purine] luminesces via ligand-to-metal energy transfer (Chapter 5).