Interpretation of DNA vibration modes: I-The guanosine and cytidine residues involved in poly(dG-dC)·poly(dG-dC) and d(CG)₃·d(CG)₃

Abstract

A normal coordinate analysis has been carried out on guanosine and cytidine residues appearing in oligo and polynucleotides by using a simplified valence force field that allows the vibrational spectra of 5'-dGMP and 2'-deoxycytidine molecules to be reproduced. The role of both C2'-endo and C3'-endo conformations on sugar pucker, as well as that of glycosidic torsion angle (X), on several characteristic vibration modes of these residues have been studied. The present calculations based on a non-redundant set of internal coordinates preserving the harmonic approximation of the potential field, allows us to explain quite satisfactorily the modifications of the vibrational spectra in the 1550-1250 cm-1 and 785-500 cm-1 regions, when the right----left-handed conformational transition occurs.

Fourier Transform Infrared Spectroscopy of the DNA of the Chuxiong Population ofCamellia reticulataLindl. of China

“…The peak at 1382 cm À1 is assigned to guanosine for the glycosyl torsion angle x in anticonformation, and the peak at 1411 cm À1 is assigned to the C2-endo deoxyribose vibration. [27,[37][38][39] The bands in the region of 1750-1500 cm À1 are related to the GÀC and AÀT base-pairs. [13,32,38] The peak at 1665 cm À1 is due to C2=O2 vibrations of base-pairing of cytosine bases.…”

“…The band at 1382 cm À1 is assigned to guanosine for the glycosyl torsion angle x in anticonformation, and the band at 1411 cm À1 is due to, [27] C2 0 -endo to C3 0 -endo. [33,[37][38][39] The bands in the region of 1750-1500 cm À1 are related to the GÀC and AÀT base-pairs. [2,11,13,15,27,32,39,40] Therefore, DNA FTIR of varieties of Chuxiong population of C. reticulata Lindl.…”

Selected deoxyoctanucleotides and their daunomycin complexes: Infrared absorption and vibrational circular dichroism spectra

“…The absorption at 1684 cm À1 and the corresponding VCD couplet at 1692(À)/1678(+) cm À1 dominate the spectra. These bands can be assigned confidently to the carbonyl vibration of G in the Cy-Gu base pair in the B conformation [28,30,31]. They are similar to those of poly(dG-dC)Ápoly(dGdC) [14,20] as well as 5 0 d(CGCG) 30 [18] with absorptions at 1693 and 1685 cm À1 and correspond to VCD couplets at 1700(À)/ 1670(+) and 1694(À)/1679(+) cm À1 , respectively.…”

“…The D 2 O absorbance between 1300 and 1200 cm À1 obscures the PO 2 À asymmetric stretch, which normally occurs around 1220 cm À1 . Absorptions near 1076, 1055, 1022, 972, 945 and 895 cm À1 are ascribed to deoxyribose [30][31][32][33][34].…”

“…Tables 1 and 2 list the observed absorption and VCD peaks of the free deoxyoctanucleotides and their corresponding daunomycin complexes. Absorptions of DNA and individual components have been investigated previously [25][26][27][28][29][30][31][32][33][34][35]. Assignments based on ab initio derived harmonic force field calculations have been made for nucleobases, deoxyribose, phosphate, and for several deoxyoctanucleotides [36][37][38][39][40][41][42][43].…”