Vibrational circular dichroism of deoxyoligonucleotides

Thesis/Dissertation · Fri Jan 01 04:00:00 EST 1993

OSTI ID:7044823

Gulotta, M S

In this thesis, infrared (vibrational) circular dichroism (VCD) is shown to be a viable technique for examining the secondary structure of deoxyoligonucleotides. In these studies spectra were taken in the 1550--1750 cm[sup [minus]1] carbonyl stretching region. VCD spectra of the low salt conformations of poly(dG)poly(dC), poly(dG-dC)poly(dG-dC), poly(dG-me[sup 5]dC)poly(dG-me[sup 5]dC), and pd(CG)[sub 5] are examined. The B-form VCD spectrum of a GC-deoxyoligonucleotide is characterized by a negative/positive couplet at approximately 1700 cm[sup [minus]1] and 1680 cm[sup [minus]1] respectively. High salt Z-form spectra of poly(dG-dC)poly(dG-dC) and poly(dG-me[sup 5]dC)poly(me[sup 5]dC) are also presented. The author has found that the VCD spectra of poly(dG-dC)poly(dG-dC) and poly(dG-me[sup 5]dC)poly(dG-me[sup 5]dC) in high salt solution varies depending on whether NaCl or MgCl[sub 2] is used to induce the B-Z transition. Left-handed conformations are characterized by a positive/negative couplet which is shifted to lower wavenumbers than the B-form couplet. The Degenerate Extended Coupled Oscillator (DECO) model is used as a means of interpreting the VCD experimental data. From the cartesian coordinates of the carbonyl groups and applying simple coupled oscillator theory, the model determines the interaction energy between these groups as well as the effect of the interactions on the dipole and rotational strengths. From the output of the model, calculated spectra can be generated. The DECO model is shown to account for the B-form VCD spectra but the model is unable to account for the Z-form spectra. The author has attributed the problems with the Z-form calculations to interactions between the oligonucleotide and the salt solution which are not currently taken into account.

• Research Organization: City Univ. of New York, NY (United States)
• OSTI ID: 7044823
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
400102* -- Chemical & Spectral Procedures
550200 -- Biochemistry
59 BASIC BIOLOGICAL SCIENCES
AMINES
AROMATICS
AZAARENES
AZINES
CONFORMATIONAL CHANGES
DEOXYCYTIDINE
DICHROISM
DNA
ENERGY LEVELS
EXCITED STATES
GUANINE
HETEROCYCLIC COMPOUNDS
HYDROXY COMPOUNDS
MOLECULAR BIOLOGY
MOLECULAR STRUCTURE
NUCLEIC ACIDS
NUCLEOSIDES
NUCLEOTIDES
OLIGONUCLEOTIDES
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
PURINES
PYRIMIDINES
RIBOSIDES
VIBRATIONAL STATES