On the Cooperativity Effect in Watson and Crick and Wobble Pairs for a Halouracil Series and Its Potential Quantitative Application Studied through Surface-Enhanced Raman Spectroscopy

The nature of the cooperativity effect of hydrogen bonds in Watson and Crick and wobble base pairs formed with thymine, uracil, and its 5-halogenated derivatives (5-fluoro, -chloro, and -bromouracil) has been studied through SERS and by using chemometric tools to process data and extract relevant in...

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Bibliographic Details
Published in:Analytical chemistry (Washington) 2018-12, Vol.90 (24), p.14165-14172
Main Authors: Mamián-López, Mónica B, Temperini, Marcia L. A
Format: Article
Language:English
Subjects:
Analytical chemistry
Base Pairing
Base pairs
Bromouracil - analysis
Chemistry
Cooperativity
Data processing
Deoxyribonucleic acid
DNA
Gold - chemistry
Hydrogen bonding
Hydrogen bonds
Information processing
Least-Squares Analysis
Limit of Detection
Metal Nanoparticles - chemistry
Nucleic Acid Conformation
Principal Component Analysis
Raman spectroscopy
Spectroscopy
Spectrum analysis
Spectrum Analysis, Raman - methods
Stability analysis
Thymine
Thymine - chemistry
Thymine - metabolism
Uracil
Uracil - chemistry
Uracil - metabolism
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Summary:The nature of the cooperativity effect of hydrogen bonds in Watson and Crick and wobble base pairs formed with thymine, uracil, and its 5-halogenated derivatives (5-fluoro, -chloro, and -bromouracil) has been studied through SERS and by using chemometric tools to process data and extract relevant information. Remarkable differences between the two kinds of pairs were clearly observed, and the behavior correlated to the withdrawing character of different substituents at the 5-position of uracil was verified. Multivariate analyses have also unveiled information about the pair’s stability, and a stronger cooperativity effect seems to rule the Watson and Crick pairs when compared to wobble pairs. Defined patterns in the behavior of Watson and Crick pairs allowed the design of an indirect methodology for quantifying 5-bromouracil using a partial least squares (PLS) method with variable selection. Limit of detection (LOD) values of 0.037 and 0.112 mmol L–1 in the absence and presence of structurally similar interferences were reached, while its direct surface-enhanced Raman spectroscopy (SERS) quantification is only possible at ∼45 mmol L–1.
ISSN:0003-2700
1520-6882
DOI:10.1021/acs.analchem.8b02188