A SERS probe of adenyl residues available for intermolecular interactions. Part I—adenyl ‘fingerprint’

Abstract

This work validated a SERS probe able to compare adenyl reactivity in DNA and RNA. A Creighton silver colloid including adenine (A) [or 2 -deoxyadenosine 5 -phosphate (pdA)] from 2 × 10 −3 to 2 × 10 −8 M is stabilized in the absence or presence of chloride. Concentration-dependent SER spectral profiles reveal how A may interact with (Ag) n + sites. At concentration ≥2 × 10 −5 M adsorption of (A) n clusters prevents the colloid from undergoing salt effects. Adsorption via N1/N3 is allowed whereas C6NH 2 is involved in self-association. At [A] <2 × 10 −5 M with chloride, hydrogen bonding between chloride and the C6NH 2 group enhances C6N electronegativity, which assists C6N/N7 cooperative adsorption. Complex A(Cl − ) entities compete with individual chloride ions for adsorption on silver. Very similar C6N/N7 adenyl adsorption occurs for pdA but only above 2 × 10 −5 M. Chloride-adenyl bonding is reduced and pdA self-association is weaker than adenine self-association. Steric factors, repulsive electrostatic forces and phosphate competitive reactivity with respect to chloride may explain the much higher pdA concentration needed to saturate the silver surface compared with A. Mg 2+ -phosphate complexation entails concentration-dependent opposite effects on adenyl reactivity with (Ag) n + sites. Cytosine, thymine and guanine base or corresponding nucleotides deliver weaker SER spectra and much higher SERS responses for chloride adsorption compared with A or pdA. This reveals a weaker adsorption of the oxo bases, assumed to result from alternative oxo and nitrogen interactions with the (Ag) n + sites.

Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy

“…Since the responses of adenine and pdA (5 0 -monophosphate deoxy adenosine) were dramatically greater than those of the other bases and mononucleotides, we concluded that the reactivity of adenine and adenyl residues with the silver electropositive sites is much greater than that of the other nucleic bases or base residues. 41 The similar SER spectral profile obtained for adenine, pA (5 0 -monophosphate adenosine), pdA, dA tracts, and A in r and d-hairpins in the 2 Â 10 À6 to 2 Â 10 À8 M concentration (c) ranges prove that adenine and adenyl residues bind similarly to [Ag] þ n . [41][42][43] Only the relative spectral intensities varied, which are representative of different amounts of A loaded on [Ag] þ n (A-loading).…”

“…41 The similar SER spectral profile obtained for adenine, pA (5 0 -monophosphate adenosine), pdA, dA tracts, and A in r and d-hairpins in the 2 Â 10 À6 to 2 Â 10 À8 M concentration (c) ranges prove that adenine and adenyl residues bind similarly to [Ag] þ n . [41][42][43] Only the relative spectral intensities varied, which are representative of different amounts of A loaded on [Ag] þ n (A-loading). At a given concentration, the greater the load the more A is assumed to be reactive.…”

“…41,42 The number of accessible [Ag] þ n SER-active sites could be fewer but the SER-exciting laser line (488 nm) better tuned with the plasmon transition. 41,42,49 With NaCl and MgCl 2 too, plasmon spectra were relatively independent of the nucleic acid present and its concentration. 41,42 Silver plasmon absorbance for triplicate did not vary by more than 6 5%.…”

“…To measure Mg 2þ effects on A reactivity with SERS, MgCl 2 was added in place of NaCl to the probing silver colloid. 41,42 The present paper combines new and previous SER data [41][42][43] aimed at correlating primary and secondary structures with A reactivity in the presence of biological amounts of Cl -and Na þ or Mg 2þ ions. A reactivity in pA, (pA) n [r poly(A)] and (pA) n Á (pU) n [r poly(U)] and d counterparts pdA, (pdA) n , and (pdA) n Á (pdT) n [d poly(A) and poly(dT)] is compared to the reactivity of adenine.…”

“…1 We have developed a surface-enhanced Raman spectroscopy (SERS) method to measure and rank the reactivity of A residues in d and r nucleic acid constructs in which secondary structures are characterized. [41][42][43] The probe used for measuring A reactivity is a conventional Creighton silver colloid. 44 The average radius of the silver particles is $ 30 nm.…”