Effect of salt concentration on the stability of heterogeneous DNA

Singh, Awatar; Singh, Navin

doi:10.1016/j.physa.2014.10.029

Cited by 41 publications

(31 citation statements)

References 53 publications

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“…The stability of double stranded DNA (dsDNA) can be affected by temperature, pH and ionic composition of solution (solvent)[19]. Salting-out has proven to be a cost-effective method for extracting DNA from whole blood, which gives good DNA yield for downstream analyses[20,21].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of DNA extracted from blood filter spots and eluates processed for enzyme linked immunosorbent assay (ELISA)

Xatse

Akorli

Owusu

et al. 2019

Preprint

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15Dried filter blood spots have become a significant blood collection method for screening 16 individuals for clinical purposes. When used for ELISAs, they are normally discarded after the 17 blood has been eluted. However, they may still be useful for extraction of DNA for molecular-18 based assays. The aim of this work was to determine the integrity of DNA extracted from filter 19 paper spots from which blood has initially been eluted for ELISA with sample dilution buffer 20 (SDB) and phosphate buffered saline (PBS). DNA was extracted from the eluted filter spots, the 21 eluate, and dried blood filter spots (controls) using spin column extraction. The quality and 22 quantity of the extracted DNA was assessed and used for PCR to further evaluate their 2 23 usefulness in molecular assays. Concentration of DNA obtained was dependent on the buffer 24 used for processing the filter blood blots. Accounting for the DNA concentration obtained from 25 dried blood spots, which were used as controls, DNA extracted from the already eluted blood 26 spots were 32 times higher in PBS than SDB processed filter paper. The ratio was even higher 27 for the eluates, which were 57 times higher in PBS than SDS eluates. SDB eluates had 28 significantly higher average DNA concentration than their eluted filter paper, but their purity 29 ratios were similar. 85% PCR success rate was achieved with the DNA samples. Useful DNA 30 can be extracted from blood spots after it has been eluted with SDB. Although the DNA 31 concentration and purity may be low, the DNA could be useful for rather simple PCR assays. 32 Author Summary 33Collection of blood onto filter paper has become an accepted method for screening individuals 34 for clinical and public health purposes since the 1960s. This method of blood collection has 35 become increasingly popular due to its ease and convenience in collection and transportation. 36The use of dried blood spots for clinical evaluations and research has become very significant. 37For research purposes, DBS when used for ELISAs are discarded after single use. DNA may 38 however be extracted from the used filter blots and used for molecular assays. The concentration 39 of DNA obtained may be low but simple assays like PCR could be done using the DNA 40 extracted from the eluted filter spot. 41 96 paper). DNA was extracted from the eluate, eluted filter paper and the dried unprocessed DBS 97 using the Qiagen DNA Blood and Tissue kit according to the manufacturer's instruction. DNA 98 was eluted in 150 µL of buffer AE. DNA quantity and purity were measured using Qubit ® 2.0 6 99 fluorometer (Invitrogen, Life technologies) and NanoDrop 2000c Spectrophotometer (Labtech 100 International Ltd, Thermo Scientific, UK). Samples were stored at −40°C for further analysis. 101 Amplification of human ribosomal gene 102 PCR was performed to evaluate the quality of genomic DNA extracted. A 231bp region of the 103 small subunit of human ribosomal gene (ssrDNA) was amplified [16,17] UNR-HUF, 5'-104 GAGCCGCCTGGATACCGC-3' REV, ...

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Section: Discussionmentioning

confidence: 99%

Evaluation of DNA extracted from blood filter spots and eluates processed for enzyme linked immunosorbent assay (ELISA)

Xatse

Akorli

Owusu

et al. 2019

Preprint

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“…For example, in somatic cells the concentrations of sodium ions substantially increase during activation to become cancer cells [1,52]. From most of the previous studies it was concluded that these cations contribute to the stability of the DNA in the cell [28,33]. These cations act as shielding agents for the negatively charged strands of DNA.…”

Section: Discussionmentioning

confidence: 99%

“…For the current investigations we adopt the standard Peyrard Bishop Dauxois (PBD) model [26,27] and modify the potentials appearing in the model. In our earlier work, we showed that the PBD model has enough detail to explain the thermal as well as mechanical stability of DNA molecules at lower strengths of salt and with varying salt concentration [5,28]. Our presentation in the current manuscript is organized as follows.…”

Section: Introductionmentioning

confidence: 99%

Differential stability of DNA based on salt concentration

Maity

Singh

2016

Eur Biophys J

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Intracellular positive ions neutralize negative charges on the phosphates of a DNA strand, conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a certain value of salt concentration, the DNA molecule displays an unstable nature in vivo as well as in vitro. We consider a wide range of salt concentrations and study the stability of the DNA double helix using a statistical model. Through numerical calculations, we attempt to explain the different behavior exhibited by DNA molecules in this range. We compare our results with experimental data and find a close agreement.

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“…The sequence heterogeneity has effect on the stacking interaction along the strand. This can be taken care of through the single strand elasticity parameter k. One can take the variable k according to the distribution of bases along the strand [31]. A defect in a pair will modify the electronic distribution around the bases hence the stacking parameters.…”

Section: The Modelmentioning

confidence: 99%

Pulling short DNA molecules having defects on different locations

Singh

2015

Phys. Rev. E

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We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects that occurs anywhere in the molecule. For the investigation, we consider four different kinds of chains. Not only the ratio of AT to GC different in these molecules but also the distributions of AT and GC along the molecule are different. With suitable modifications in the statistical model to show the defect in a pair, we investigate the denaturation of short DNA molecules in thermal as well as constant force ensemble. In the force ensemble, we pulled the DNA molecule from each end (keeping other end free) and observed some interesting features of opening of the molecule in the presence of defects in the molecule. We calculate the probability of opening of the DNA molecule in the constant force ensemble to explain the opening of base pairs and hence the denaturation of molecules in the presence of defects.

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Effect of salt concentration on the stability of heterogeneous DNA

Cited by 41 publications

References 53 publications

Evaluation of DNA extracted from blood filter spots and eluates processed for enzyme linked immunosorbent assay (ELISA)

Evaluation of DNA extracted from blood filter spots and eluates processed for enzyme linked immunosorbent assay (ELISA)

Differential stability of DNA based on salt concentration

Pulling short DNA molecules having defects on different locations

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