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On the Study of Matched and Mismatched Nucleobase Pairs by Using Raman Spectroscopy

Author: LiaoZuoBo
Tutor: MengYaoYong
School: South China Normal University
Course: Optics
Keywords: Raman spectroscopy Polynucleotide Base pairing Base mismatch
CLC: O433
Type: Master's thesis
Year: 2007
Downloads: 55
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Abstract

Along with the smooth implementation of the Human Genome Project, gene chip for the pilot bio-chip technology has been rapid development has attracted wide attention in the international community. The gene chip technology needs to accurately predict the number and types of paired bases and unpaired bases. Thus an urgent need for a sensitive, accurate and convenient means of detection with suitable. At present, the gene chip signal detection in fluorescence detection. Nucleic acid fluorescence detection requires a combination of fluorescent markers. This mark is incomplete, non-specific adsorption of the targets, fluorescence bleaching, quenching and background interference and other shortcomings. In addition, the fluorescence band is relatively wide, not suitable for multiple testing. Than the fluorescence detection, laser Raman spectroscopy method without sample tags, to provide spectral information about the molecular structure of the sample, and the peaks fine sharp for easy identification. Additionally, it is almost not subject to the interference of an aqueous solution, especially suitable for the detection of biological samples. Therefore, the laser Raman spectroscopy is a promising bio-chip detection method. Composite synthetic polynucleotide PolyA, PolyU, PolyG the PolyC and between them is formed by laser Raman spectroscopy test, and to examine the variation of the spectrum before and after the formation of the composite. It was found that the nucleotide complementary single-stranded nucleic acid is formed between the Raman spectrum showing the characteristics of a distinct change in the composite PolyA PolyU and PolyG · PolyC. First, the characterization of the main chain conformation of the A-type Raman peak 810 cm ^{-1 -815cm ^{-1 increase in the relative intensity of R parameters used to describe the degree of ordering of the main chain conformation (R = I ₈₁₀ / I ₁₁₀₀) increases, before pairing composite random coil or single-stranded helix, the complex has formed a double helix structure morphology; Secondly, with respect to the single-stranded random coil state, the double helix is ??formed such that 1100 cm ^{-1 half-height peak width is narrowed; again, complementary base pairing the one hand makes the formation of double-stranded Characterization of the structure of the hydrogen bonding ligand group occurs a significant change from the original carbonyl such as Polyu PolyC exposure status changes to \Group associated with hydrogen-bonding sites vibration frequency also changes. On the other hand, it perpendicular to the base - base stacking force has greatly increased, the main chain conformation becomes more orderly, resulting in a obvious Raman subtractive effect and accompanied by a frequency shift of the bands. In addition, we also have a composite of the two base mismatch. The results showed that non-between complementary bases with complementary bases by hydrogen bonding interactions. Raman spectral characteristics and formation of complexes between different bases and different. This was reflected in: First, while PolyG · PolyA PolyA · PolyC form the double helix structure characterization of the spiral structure of the A-type bands fall 810cm ^{-1 and 806cm ^{-1, . But the latter also characterize the B-type structure 836cm ^{-1 peak. The emergence of the peak PolyA · PolyC is not typical A-type conformation, but should be defined as A / B and Chief type. Secondly, GA composite 1090cm ^{-1 near the doublet, and therefore corresponds to two R values ??with the degree of ordering of the two chains in the double helix. After the formation of the complex, poly-G chain, poly (A) chain has hardly changed. AC complex pairing case. Again, study 1099cm ^{-1 FWHM, we found PolyA · PolyC where the line width of 33cm ^{-1 , complementary base complexes similar. However PolyG · PolyA compared to 61 cm ^{-1 , significantly wider, which may and PolyG distorted main chain. In addition, the compound of AC resulted in obvious \Poly-G · Polya, however, although some bands also showed strength weakening, but there are many characterization of base stacking band intensity, in particular, the adenine band has not only weakened, but greatly enhanced. This is also the G-A fault with a major feature. Finally, the composite of the two base mismatch. Hydrogen coordination modes are also very different. The AC composite contains only a base hydrogen; GA compound in addition to the hydrogen-bonding ligand point of the two bases, the base ring of the main chain between the presence of a hydrogen bond. The experimental results show that not only Raman spectrum of hydrogen bonding ligand for the study of nucleic acids, the main chain conformation and base stacking is a strong tool. Moreover, in view of the Raman spectra reflect the subtle changes of the molecular structure, without marking, sample preparation is simple, quick test, the peak fine sharp superiority, it is expected to be a promising gene microarray technology.}}}}}}}}}}

On the Study of Matched and Mismatched Nucleobase Pairs by Using Raman Spectroscopy

Abstract

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