Vibrational analysis of the hydrogen bonding of cytidine and guanosine derivatives

Abstract

Hydrogen bonding between 2′-deoxy-3′,5′-bis(triisopropylsilyl)guanosine (G) and 2′-deoxy-3′,5′-bis(triisopropylsilyl)cytidine (C) has been studied by vibrational spectroscopy in chloroform solution. Strong interactions occur between the two derivatives of guanosine and cytidine and between CG base pair and cytidine, whose association constants were first determined. CGC trimers involve cyclic hydrogen bonds through the N(3) acceptors of both nucleobases and the guanine N(2)H and cytosine N(4)H donors. The main spectral changes of CG dimer accompanying CGC trimer formation are intensity and frequency decreases of the Raman band of guanine base near 1570 cm-1 as well as downshifting of the 1534-cm-1 Raman band of the cytosine base that binds to the previously formed CG base pair. Similar spectral changes are observed for the infrared bands located near these frequencies. The 1483-cm-1 band of guanine is sensitive to hydrogen bonding at the N(7) position. Since this band is unchanged when the CG dimer is converted to the CGC trimer, it is concluded that no binding at the G(7) position occurs in the trimer. Raman spectroscopy can, then, distinguish between hydrogen bonds involving guanine N(7) and N(3) acceptors and offers prospect for determining these specific interactions in polynucleotide triplexes and nucleic acid-protein recognition. © 1993 American Chemical Society.