Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches.

Chemical Science
Luciana M. OliveiraGerald Weber

Abstract

Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bonding and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied in varying experiments or theoretical models. Here, we report on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch combinations, including single, double and triple mismatches were covered. These were compared with 64 sequences containing all combinations of canonical base pairs in the same location under the same conditions. For a substantial number of single mismatch configurations, 15%, the measured melting temperatures were higher than the least stable AT base pair. The mesoscopic calculation, using the Peyrard-Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on-site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking. Our results confirm many of the known properties of m...Continue Reading

References

Dec 20, 1992·Journal of Molecular Biology·J W ChengB R Reid
Jul 30, 1991·Biochemistry·Y LiW D Wilson
Jan 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·Y LiW D Wilson
Oct 11, 1990·Nucleic Acids Research·G A LeonardT Brown
May 20, 1989·Journal of Molecular Biology·T BrownJ Chambers
Oct 1, 1986·Journal of Biomolecular Structure & Dynamics·W N HunterO Kennard
Jun 15, 1995·European Journal of Biochemistry·A N Lane, B Peck
Apr 13, 1993·Biochemistry·K MaskosK M Morden
Feb 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·J V SkellyS Neidle
Jan 1, 1996·Annual Review of Biochemistry·P Modrich, R Lahue
Jun 15, 1997·Nucleic Acids Research·M Mitas
Aug 26, 1997·Biochemistry·H T Allawi, J SantaLucia
Mar 28, 1998·Biochemistry·H T Allawi, J SantaLucia
Aug 1, 1998·The Journal of Biological Chemistry·T R Waters, P F Swann
Jun 5, 1989·Physical Review Letters·M Peyrard, A R Bishop
Nov 3, 2001·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·N Singh, Y Singh

❮ Previous
Next ❯

Citations

Feb 21, 2021·Molecular and Cellular Probes·Pâmella Miranda, Gerald Weber
Mar 5, 2021·Biophysical Chemistry·Izabela FerreiraGerald Weber
Apr 7, 2021·Nucleic Acids Research·Nick A RejaliCarl T Wittwer
Jul 13, 2021·Journal of Chemical Information and Modeling·Izabela FerreiraGerald Weber

❮ Previous
Next ❯

Methods Mentioned

BETA
scanning differential calorimetry
X-ray
nuclear magnetic resonance
NMR
deamination
PCR

Software Mentioned

MutS
TfReg

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.