Determination of Base Binding Strength and Base Stacking Interaction of DNA Duplex Using Atomic Force Microscope

Zhang, Tianbiao; Zhang, Chang-lin; Dong, Zaili; Guan, Yifu

doi:10.1038/srep09143

Cited by 33 publications

(22 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Interactions outside the DNA double helix generally play a less important role [ 160 ]. The interplay between hydrogen bonding and stacking interactions in DNA has been the subject of several experimental [ 161 , 162 , 163 , 164 , 165 ] and theoretical investigations [ 159 , 166 , 167 , 168 , 169 , 170 , 171 , 172 , 173 ]. Based on DNA melting and energetics of the double helix [ 174 ], it has been recently suggested that in accordance with previous experiments [ 165 , 175 ] the stability of DNA double strands depends mainly on G-C base pair rich sequences.…”

Section: Conclusion and Outlookmentioning

confidence: 99%

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

2021

View full text Add to dashboard Cite

In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)–thymine (T), adenine (A)–uracil (U) and guanine (G)–cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N–H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O–H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C–H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C–H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N–H⋯N bond and the C–H⋯O bonds, and at the same time decreases the strength of the N–H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.

show abstract

Section: Conclusion and Outlookmentioning

confidence: 99%

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

2021

View full text Add to dashboard Cite

show abstract

“…The universal anchor sequence length was increased by 5 nt on the 5’ end relative to the sequence reported by Todhunter et al 36 in order to increase duplex length 37 when hybridized to the detection oligonucleotide, which was also purchased from IDT. The detection oligonucleotide was based on the Arabidopsis thaliana FRK1 gene because of its lack of sequence homology with human and viral genes.…”

Section: Methodsmentioning

confidence: 99%

Toward Community Surveillance: Detecting Intact SARS-CoV-2 Using Exogeneous Oligonucleotide Labels

Carey

Kozminsky

Hall

et al. 2021

Preprint

View full text Add to dashboard Cite

The persistence of the COVID-19 pandemic demands a dramatic increase in testing efficiency. Testing pooled samples for SARS-CoV-2 could meet this need; however, the sensitivity of RT-qPCR, the gold standard, significantly decreases with an increasing number of samples pooled. Here, we introduce DIVER, a method that quantifies intact virus and is robust to sample dilution. DIVER first tags viral particles with exogeneous oligonucleotides, then captures the tagged particles on ACE2-functionalized beads, and finally quantifies the oligonucleotide tags using qPCR. Using spike-presenting liposomes and Spike-pseudotyped lentivirus as SARS-CoV-2 models, we show that DIVER can detect 1x105 liposomes and 100 pfu lentivirus and can successfully identify positive samples in pooling experiments. Overall, DIVER is well-positioned for efficient sample pooling and expanded community surveillance.

show abstract

“…In combination with standard wide-field or total internal reflection microscopy the spatiotemporal distribution of forces can be determined at high resolution, which is only limited by the optical resolution (~0.2 µm). The mechanical stability of dsDNA depends on its length and the GC content (Zhang et al, 2015). The force F1/2 that is required to unfold 50% of the DNA sensors, has been calibrated in previous single-molecule studies between ~4-60 pN for varying DNA sequences (Wang and Ha, 2013;Zhang et al, 2014).…”

mentioning

confidence: 99%

An in vitro DNA Sensor-based Assay to Measure Receptor-specific Adhesion Forces of Eukaryotic Cells and Pathogens

et al. 2020

View full text Add to dashboard Cite

Motility of eukaryotic cells or pathogens within tissues is mediated by the turnover of specific interactions with other cells or with the extracellular matrix. Biophysical characterization of these ligandreceptor adhesions helps to unravel the molecular mechanisms driving migration. Traction force microscopy or optical tweezers are typically used to measure the cellular forces exerted by cells on a substrate. However, the spatial resolution of traction force microscopy is limited to ~2 µm and performing experiments with optical traps is very time-consuming. Here we present the production of biomimetic surfaces that enable specific cell adhesion via synthetic ligands and at the same time monitor the transmitted forces by using molecular tension sensors. The ligands were coupled to double-stranded DNA probes with defined force thresholds for DNA unzipping. Receptor-mediated forces in the pN range are thereby semi-quantitatively converted into fluorescence signals, which can be detected by standard fluorescence microscopy at the resolution limit (~0.2 µm). The modular design of the assay allows to vary the presented ligands and the mechanical strength of the DNA probes, which provides a number of possibilities to probe the adhesion of different eukaryotic cell types and pathogens and is exemplified here with osteosarcoma cells and Plasmodium berghei Sporozoites.

show abstract

Determination of Base Binding Strength and Base Stacking Interaction of DNA Duplex Using Atomic Force Microscope

Cited by 33 publications

References 30 publications

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study

Toward Community Surveillance: Detecting Intact SARS-CoV-2 Using Exogeneous Oligonucleotide Labels

An in vitro DNA Sensor-based Assay to Measure Receptor-specific Adhesion Forces of Eukaryotic Cells and Pathogens

Contact Info

Product

Resources

About