Raman spectroscopic measurements in self-pressurized aqueous solutions above 100�C: The melting of poly(G) and poly(G) � poly(C)

Mercier, Pascal; Carrier, Virginie; Roy, Sougata; Savoie, Rodrigue

doi:10.1002/(sici)1097-0282(199901)49:1<21::aid-bip3>3.0.co;2-y

Cited by 8 publications

(5 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…One possibility is to separately analyze individual spectral parameters of Raman bands using an analogous fit. [ 17–22 ] However, the method is relatively inconvenient. The result of the fit is influenced by limited precision of the analyzed data given by the experimental error, uncertainties in the subtraction of the background signal, and/or the effects of overlapping bands.…”

Section: Introductionmentioning

confidence: 99%

Full UV resonance Raman analysis of temperature effects on the structural arrangement of DNA segments

Klener

Štěpánek

2020

J Raman Spectroscopy

View full text Add to dashboard Cite

Temperature dependence of vibrational spectra provides important information about the geometry and stability of nucleic acid segments. Even in cases of simple structural transitions between the folded and unfolded states, three types of spectral changes may occur – the actual structural transition, the influence of temperature change on the oligonucleotide in the folded state, and that in the unfolded state. In this work, the temperature dependences of UV resonance Raman spectroscopy (RRS) spectra excited at 244 and 257 nm were measured on two dodecadeoxynucleotides, duplex and hairpin. In both cases, the total base composition was the same, containing (in the folded state) a double‐strand section of guanine‐cytosine (GC) pairs and a central section of adenine‐thymine (AT) pairs forming a flexible part of the double helix in the duplex or the loop in the hairpin. Principal component analysis (PCA) showed that UV RRS spectrum, unlike non‐resonance RS, can reliably distinguish between the three types of temperature changes. Spectral images of the changes confirmed the B‐form double helix of GC sections in both the duplex and hairpin and different base positions in AT base sections. Additionally, minimal stacking interactions between the bases in the loop and other types of interactions of adenine with the bases of the stem in the hairpin were shown, and the main effects of heating in the folded state on the GC sections manifested weakening of stacking interactions. The results demonstrate UV RRS potential for studies of non‐canonical nucleic acid structures, providing properly analyzed and executed measurements of temperature dependence.

show abstract

Section: Introductionmentioning

confidence: 99%

Full UV resonance Raman analysis of temperature effects on the structural arrangement of DNA segments

Klener

Štěpánek

2020

J Raman Spectroscopy

View full text Add to dashboard Cite

show abstract

“…Since that time, dramatic improvements in the versatility and sensitivity of Raman instrumentation have greatly enhanced the potential of the method (19,21,22). In recent years, studies of thermally induced structural changes of DNA have combined the data of Raman spectroscopy with other approaches, including DSC (19), sequence analysis (29), ultraviolet-resonance Raman (UVRR) spectroscopy (30), CD and Fourier-transform infrared (FTIR) spectroscopies (31) and superheating of solutions at high pressure (32).…”

Section: Introductionmentioning

confidence: 99%

Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B DNA

Movileanu¹

2002

Nucleic Acids Research

View full text Add to dashboard Cite

In previous papers of this series the temperature-dependent Raman spectra of poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) were used to characterize structurally the melting and premelting transitions in DNAs containing consecutive A.T and alternating A.T/T.A base pairs. Here, we describe procedures for obtaining thermodynamic parameters from the Raman data. The method exploits base-specific and backbone-specific Raman markers to determine separate thermodynamic contributions of A, T and deoxyribosyl-phosphate moieties to premelting and melting transitions. Key findings include the following: (i) Both poly(dA).poly(dT) and poly(dA-dT). poly(dA-dT) exhibit robust premelting transitions, due predominantly to backbone conformational changes. (ii) The significant van't Hoff premelting enthalpies of poly(dA).poly(dT) [DeltaH(vH)(pm) = 18.0 +/- 1.6 kcal x mol(-1) (kilocalories per mole cooperative unit)] and poly(dA-dT).poly(dA-dT) (DeltaH(vH)(pm) = 13.4 +/- 2.5 kcal x mol(-1)) differ by an amount (approximately 4.6 kcal x mol(-1)) estimated as the contribution from three-centered inter-base hydrogen bonding in (dA)(n).(dT)(n) tracts. (iii) The overall stacking free energy of poly(dA). poly(dT) [-6.88 kcal x mol(bp)(-1) (kilocalories per mole base pair)] is greater than that of poly(dA-dT). poly(dA-dT) (-6.31 kcal x mol(bp)(-1)). (iv) The difference between stacking free energies of A and T is significant in poly(dA).poly(dT) (DeltaDeltaG(st) = 0.8 +/- 0.3 kcal. mol(bp)(-1)), but marginal in poly(dA-dT).poly(dA-dT) (DeltaDeltaG(st) = 0.3 +/- 0.3 kcal x mol(bp)(-1)). (v) In poly(dA). poly(dT), the van't Hoff parameters for melting of A (DeltaH(vH)(A) = 407 +/- 23 kcal.mol(-1), DeltaS(vH)(A) = 1166 +/- 67 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(A) = 60.0 +/- 3.2 kcal x mol(-1)) are clearly distinguished from those of T (DeltaH(vH)(T) = 185 +/- 38 kcal x mol(-1), DeltaS(vH)(T) = 516 +/- 109 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(T) = 27.1 +/- 5.5 kcal x mol(-1)). (vi) Similar relative differences are observed in poly(dA-dT). poly(dA-dT) (DeltaH(vH)(A) = 333 +/- 54 kcal x mol(-1), DeltaS(vH)(A) = 961 +/- 157 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(A) = 45.0 +/- 7.6 kcal x mol(-1); DeltaH(vH)(T) = 213 +/- 30 kcal x mol(-1), DeltaS(vH)(T) = 617 +/- 86 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(T) = 29.3 +/- 4.9 kcal x mol(-1)). The methodology employed here distinguishes thermodynamic contributions of base stacking, base pairing and backbone conformational ordering in the molecular mechanism of double-helical B DNA formation.

show abstract

“…The former is attributed to NH 2 scissoring of guanine ring [13] and the latter originates from carbonyl stretching of self-associated PolyG in quadruplex form. [14] Two bands of PolyC appear with frequencies at 1610 cm -1 and 1650 cm -1 , respectively. The former is mainly attributed to δ(NH 2 ) of cytosine modes.…”

Section: Resultsmentioning

confidence: 99%

Raman Spectroscopic Study of Nucleobase Pairs and Mispairs - A Potential Method for Analysis of DNA Sequences

Liao

Meng

Lei

et al. 2012

AMR

View full text Add to dashboard Cite

To exploit sensitive, accurate and convenient detection techniques for nucleic acid sequences can help to overcome the defects of current fluorescence detection method. Raman spectroscopy represents one family of methods that may offer such potential. In this paper, G•C base pairs and C•U mispairs were studied by Raman spectral characterization of single-strand homopolynucleotides, i.e. polyguanylic acid (PolyG), polycytidylic acid (PolyC) and polyuridylic acid (PolyU), and their equimolar complexes PolyG•PolyC and PolyC•PolyU in solution of 0.14 M Na+, pH7.0. Both of the complexes were found to adopt A type conformation. Helix formation between complementary polynucleotides led to marked and characterisctic changes in frequency and intensity of Raman bands of the biopolymers. Spectral changes were also observed upon the formation of C•U mispairs. According to the Raman data, in C•U mispairs the C2=O of U was engaged in a hydrogen bond to the N4H2group of cytosine, while the uracil C4=O group is free. Some of the rC residues transformed from C3-endo/anti to C2-endo/anti conformation due to base mispairing.The results suggest that Raman spectroscopy provides detailed and highly sensitive information about both the structure of nucleic acids and their base composition, and has great potential for analysis of DNA sequences.

show abstract

Raman spectroscopic measurements in self-pressurized aqueous solutions above 100�C: The melting of poly(G) and poly(G) � poly(C)

Cited by 8 publications

References 23 publications

Full UV resonance Raman analysis of temperature effects on the structural arrangement of DNA segments

Full UV resonance Raman analysis of temperature effects on the structural arrangement of DNA segments

Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B DNA

Raman Spectroscopic Study of Nucleobase Pairs and Mispairs - A Potential Method for Analysis of DNA Sequences

Contact Info

Product

Resources

About