Poly(2‐aminodeoxyadenylic acid): Circular dichroism and thermal stability of its complexes and their relevance to phage DNA in which A is replaced by 2NH₂A

Abstract

2-Aminopolyadenylic acid and its helical complexes have been thoroughly examined in the ribopolynucleotide series,1-3 but comparable information is not available in the deoxy series. The need for such information has been highlighted recently by the remarkable discovery of a new kind of DNA by Kirnos et a1.495 They have found that the DNA of cyanophage S-2L has all of its A residues replaced by 2NH2A. They have reported its thermal stability and anomalous CD spectrum and, in the absence of deoxy models, have based their interpretation on ribopolynucleotide studies2 Further biological interest in 2-aminopolydeoxyadenylic stems from the work of Stahl and Chamberlin,G who found that in T7 DNA promoter regions, 2NH2A is read as G rather than as A. The enzyme evidently recognizes the NH2 in the minor groove without reference to base pairing. Within a transcribed region, however, 2NHzA is read and transcribed as A by a base-pairing mechanism. To obtain basic chemical information relevant to biological properties of 2NH2A, we have synthesized 2-aminopolydeoxyadenylic acid and characterized its interaction with other polynucleotides. 2NH2dAMP was synthesized by the Tener p r~c e d u r e ,~ modified by addition of triethylamine to prevent the rapid depurination that occurs in the unmodified procedure. The triphosphate was made by the method of Moffatt and Khorana.s We polymerized the substrate with deoxynucleotidyl transferaseg following the procedure of Willis.l0 Synthesis of the same nucleotide and polymer has recently been reported.l1 A more detailed report of the synthetic method and physical properties will be published separately.The CD spectrum of S-2L DNA is anomalous in having two positive long-wavelength bands, a t 290 and 265 nm, rather than the usual single positive band a t -275 nm. Following the interpretation of the CD spectrum of p0ly(2NH~A).poly(U),~ which has a negative band a t 286 nm and an A-conformation, Kirnos et al.4.j attribute the long-wavelength band to the B~u transition of BNHzA, while noting the difference of sign. We find that the CD spectrum of poly(2NH2dA)-poly(dT) does indeed have a positive long-wavelength band a t 297 nm (Fig. l), identical in sign and similar in wavelength to the long-wavelength band of S-2L DNA. Reasons for assigning transitions in CD spectra of polymers containing 2NH2A residues have been presented previously in some detail.2 We follow that reasoning in the present case and assign the positive band a t 297 nm to exciton splitting of the BPU transition of 2NH2A a t -278 nm. The expected negative lobe of the splitting may contribute, presumably overlapped by a T transition, to the minimum observed at 270 nm. The

Syntheses and Base-Pairing Properties of Locked Nucleic Acid Nucleotides Containing Hypoxanthine, 2,6-Diaminopurine, and 2-Aminopurine Nucleobases

“…Importantly, much higher stabilization effects were observed when D's were involved in the formation of duplexes with a tendency to form A-type helixes (as in LNA containing duplexes 2 ). This effect has previously been shown for RNA and anhydrohexitol duplexes. The binding properties of oligonucleotides containing D's were directly studied with a microarray, a so-called generic microchip, showing both increased stabilization and mismatch discrimination .…”

Binding specificity and stability of duplexes formed by modified oligonucleotides with a 4096-hexanucleotide microarray

“…The specificity data on 2,6-diaminopurine-containing duplexes are limited by the study of duplexes with only few substitutions in complementary strands opposite replaced deoxyadenosines, indicating considerably lower stability for mismatches (18,19). Polyribonucleotides containing 2-aminoA replacements for adenosines showed a much higher stabilization effect in RNA duplexes (∼30°C) as compared to corresponding poly(2-amino-dA):poly(dT) replacements, which showed only 12°C increase in T m (20). Higher priming efficiency of (2-amino-dA)-containing oligodeoxynucleotides was succesively used in PCR experiments (21).…”

Thermodynamic studies of base pairing involving 2,6-diaminopurine

“…2-aminoadenosine (rD) and 2-amino-2'-deoxyadenosine (dD) are thought to have three hydrogen bonds with rU and dT respectively (3,(4)(5)(6)(7)(8). Thermodynamic studies on rD (4,5,(9)(10)(11)(12)(13) and dD (6,(14)(15)(16)(17) show that substitutions of rA by rD and dA by dD thermally stabilize the duplexes significantly. For example, the melting temperature (Tm) of poly(rD):poly(rU) is about 330C higher than that of poly(rA):poly(rU) in 1.0 M Na+ (5).…”