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Article ; Online: Melting of dsDNA attached with AuNPs.

Mathur, Neha / Singh, Navin

The European physical journal. E, Soft matter

2023 Volume 46, Issue 7, Page(s) 58

Abstract: DNA-linked gold nanoparticles (DNA-AuNPs) are combined nanomaterials that contain the optical and electronic properties of AuNPs with the unique functions of DNA. These hybrid systems are used in various nanobiotechnology, medical, and pharmaceutical ... ...

Abstract	DNA-linked gold nanoparticles (DNA-AuNPs) are combined nanomaterials that contain the optical and electronic properties of AuNPs with the unique functions of DNA. These hybrid systems are used in various nanobiotechnology, medical, and pharmaceutical sciences (Löwe et al. in FEBS J 287(23):5039, 2020; Speer et al. in Annu Rev Biophys 51:267, 2022). In recent years, there has been an increasing interest in studying the behavior of DNA-AuNPs in the presence of molecular solvents. In the present work, we study the thermal melting of DNA-linked gold nanoparticles (DNA-AuNP). In the first part of the study, we find the melting profile of short heterogeneous DNA-linked AuNP in the presence of solvent in the solution. We also study the effect of the location of the gold nanoparticle attached to the DNA molecule. In this case, we move the location of the AuNP from one end to the other. We found that while the melting temperature is susceptible to the location of the AuNP when it is near the ends, there is a region in the middle section of the chain where the melting temperature remains constant.
MeSH term(s)	Gold ; Metal Nanoparticles ; DNA ; Nanostructures ; Solvents
Chemical Substances	Gold (7440-57-5) ; DNA (9007-49-2) ; Solvents
Language	English
Publishing date	2023-07-21
Publishing country	France
Document type	Journal Article
ZDB-ID	2004003-9
ISSN	1292-895X ; 1292-8941
ISSN (online)	1292-895X
ISSN	1292-8941
DOI	10.1140/epje/s10189-023-00318-2
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Article ; Online: Pulling short DNA with mismatch base pairs.

Singh, Navin / Mathur, Nehal

European biophysics journal : EBJ

2023 Volume 52, Issue 3, Page(s) 145–151

Abstract: Due to misincorporation during gene replication, the accuracy of the gene expression is often compromised. This results in a mismatch or defective pair in the DNA molecule (James et al. 2016). Here, we present our study of the stability of DNA with ... ...

Abstract	Due to misincorporation during gene replication, the accuracy of the gene expression is often compromised. This results in a mismatch or defective pair in the DNA molecule (James et al. 2016). Here, we present our study of the stability of DNA with defects in the thermal and force ensembles. We consider DNA with a different number of defects from 2to16 and study how the denaturation process differs in both ensembles. Using a statistical model, we calculate the melting point of the DNA chain in both the ensemble. Our findings display different manifestations of DNA denaturation in thermal and force ensembles. While the DNA with defects denatures at a lower temperature than the intact DNA, the point from which the DNA is pulled is important in force ensemble.
MeSH term(s)	Base Pairing ; Nucleic Acid Conformation ; DNA/genetics ; Nucleic Acid Denaturation ; Temperature
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-05-30
Publishing country	Germany
Document type	Journal Article
ZDB-ID	283671-3
ISSN	1432-1017 ; 0175-7571
ISSN (online)	1432-1017
ISSN	0175-7571
DOI	10.1007/s00249-023-01659-8
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Article ; Online: Force-induced unzipping of DNA in the presence of solvent molecules.

Mathur, Neha / Singh, Amar / Singh, Navin

Biophysical chemistry

2024 Volume 307, Page(s) 107175

Abstract: The melting of double-stranded DNA (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The ...

Abstract	The melting of double-stranded DNA (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The solvents play an essential role in the structural transformation of DNA subjected to a pulling force. In this study, we simulate the thermal and force induced denaturation of dsDNA and elucidate the solvent dependent melting behavior, identifying key factors that influence the stability of DNA melting in presence of solvent molecules. Using a statistical model, we first find the melting profile of short heterogeneous DNA molecules in the presence of solvent molecules in Force ensemble. We also investigate the effect of solvent's strengths on the melting profile of DNA. In the force ensemble, we consider two homogeneous DNA chains and apply the force on different locations along the chain in the presence of solvent molecules. Different pathways manifest the melting of the molecule in both ensembles, and we found several interesting features of melting DNA in a constant force ensemble, such as lower critical force when the chain is pulled from the base pair close to a solvent molecule. The results provide new insights into the force-induced unzipping of DNA and could be used to develop new methods for controlling the unzipping process. By providing a better understanding of melting and unzipping of dsDNA in the presence of solvent molecules, this study provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA nanostructures.
MeSH term(s)	Nucleic Acid Conformation ; Models, Molecular ; DNA/chemistry ; Nucleic Acid Denaturation ; Solvents
Chemical Substances	DNA (9007-49-2) ; Solvents
Language	English
Publishing date	2024-01-11
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2024.107175
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Article ; Online: The Taq 1 polymorphism of Vitamin D receptor gene is associated with oral cancer and preoral cancer in North Indian population.

Nigam, Kumud / Singh, Navin / Yadav, Suresh Kumar / Sanyal, Somali

Journal of cancer research and therapeutics

2023 Volume 19, Issue 2, Page(s) 403–407

Abstract: Background: Oral cancer is known as one of the most common cancers, with a poor prognosis, related to delayed clinical diagnosis, either due to the lack of particular biomarkers related to the disease or costly therapeutic alternatives.: Aims and ... ...

Abstract	Background: Oral cancer is known as one of the most common cancers, with a poor prognosis, related to delayed clinical diagnosis, either due to the lack of particular biomarkers related to the disease or costly therapeutic alternatives. Aims and objectives: In this study association of single nucleotide polymorphism (Taq1, T>C) in Vitamin D receptor gene with oral cancer and pre oral cancer was studied. Materials and methods: Total 230 patients of precancerous oral lesions (Leukoplakia 70, Oral Sub mucous fibrosis 90, Lichen Planus 70), 72 oral cancer patients and 300 healthy control subjects were genotyped by PCR-RFLP methods. Chi-square test was used for calculation of genotype and allele frequencies. Results: Mutant genotype CC as well as C allele were found to significantly decrease the risk of oral disease (P value=0.04, OR=0.60 and P value=0.02, OR=0.75 respectively). In particular, compared to non smokers, smokers with TC & CC genotypes were at decrease risk of oral diseases (P value=0.0001, OR=0.04). The mutant allele genotype CC as well as the mutant allele C showed protective association with leukoplakia (P value=0.01, OR=0.39 & P value=0.009, OR=0.59 respectively). However, individual with CC genotype had developed high cell differentiated grade at diagnosis (OR= 3.78, P value= 0.008). Conclusions: This study concludes that VDR (Taq1) polymorphism is associated with oral cancer and pre oral cancer susceptibility in North Indian population.
MeSH term(s)	Humans ; Receptors, Calcitriol/genetics ; Gene Frequency ; Polymorphism, Single Nucleotide ; Genotype ; Mouth Neoplasms/epidemiology ; Mouth Neoplasms/genetics ; Precancerous Conditions ; Leukoplakia ; Genetic Predisposition to Disease ; Case-Control Studies
Chemical Substances	Receptors, Calcitriol
Language	English
Publishing date	2023-04-03
Publishing country	India
Document type	Journal Article
ZDB-ID	2187633-2
ISSN	1998-4138 ; 0973-1482
ISSN (online)	1998-4138
ISSN	0973-1482
DOI	10.4103/jcrt.jcrt_109_22
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Article: Assessment of knowledge and awareness among North Indian populations about oral precancerous lesions (OPL): A cross-sectional survey study.

Tiwari, Rini / Singh, Navin / Chaurasia, Akhilanand / Singh, Akhilesh Kumar

National journal of maxillofacial surgery

2023 Volume 14, Issue 3, Page(s) 454–459

Abstract: Background: A precancerous lesion is a morphologically altered tissue in which oral cancer is more likely to occur than its apparently normal counterpart. They are quite common in the Indian population due to the habitual habit of chewing tobacco. The ... ...

Abstract	Background: A precancerous lesion is a morphologically altered tissue in which oral cancer is more likely to occur than its apparently normal counterpart. They are quite common in the Indian population due to the habitual habit of chewing tobacco. The aim of this study was to evaluate the awareness of oral precancerous lesions by a questionnaire-based survey among the study subjects having been diagnosed with it. Methods: In this descriptive study, a structured questionnaire having 11 survey questions has been used to record the response from study subjects who have been diagnosed and reported for treatment for oral premalignant lesions in the Department of Oral Medicine and Radiology. A total of 1013 study subjects were assessed for awareness about OPL and its consequences. Results: 44.3% of the study population was addicted to smoking tobacco (cigarettes) while 57.9% of study subjects were addicted to non-smoking tobacco (Pan masala). The reason behind their addiction was reported to be stress (54.9%) and workload (25.3%). Most of the study subjects were diagnosed with oral sub-mucous fibrosis (53.4%). 78.6% of study subjects diagnosed with OPL were not aware of it and 94% were willing to quit the addiction. Conclusion: The awareness about OPL among patients was found to be low. Although many wanted to quit their addiction to smoking and chewing tobacco but were unable to do so. So it is a need for time to develop a national policy on tobacco use and related diseases. This policy will definitely reduce the burden of oral premalignant lesions and oral cancer in Indian population.
Language	English
Publishing date	2023-11-10
Publishing country	India
Document type	Journal Article
ZDB-ID	2653583-X
ISSN	2229-3418 ; 0975-5950
ISSN (online)	2229-3418
ISSN	0975-5950
DOI	10.4103/njms.njms_150_22
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Article ; Online: Structure and Dynamics of dsDNA in Cell-like Environments.

Singh, Amar / Maity, Arghya / Singh, Navin

Entropy (Basel, Switzerland)

2022 Volume 24, Issue 11

Abstract: Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA's structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely ...

Abstract	Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA's structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.
Language	English
Publishing date	2022-11-01
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2014734-X
ISSN	1099-4300 ; 1099-4300
ISSN (online)	1099-4300
ISSN	1099-4300
DOI	10.3390/e24111587
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Article: Correlation of 3DCRT and Open Field Treatment Techniques in Advanced Head and Neck Cancer Patients Treated by Chemoradiation.

Sachan, Anjali / Gupta, Seema / Singh, Navin

Journal of biomedical physics & engineering

2022 Volume 12, Issue 1, Page(s) 83–90

Abstract: Background: Multimodality treatment is required for the management of head and neck cancer. Functional impairment and toxicities associated with surgery and radiation accentuate the need to develop innovative therapeutic strategies in the management of ... ...

Abstract	Background: Multimodality treatment is required for the management of head and neck cancer. Functional impairment and toxicities associated with surgery and radiation accentuate the need to develop innovative therapeutic strategies in the management of these patients to improve survival and reduce toxicity. In this study, we have compared treatment effects in patients of advanced head and neck squamous cell cancer treated by open field and 3DCRT treatment planning techniques. Objective: This study aims to evaluate open field and 3DCRT treatment planning techniques in advanced head and neck squamous cell cancer patients managed by chemoradiation in the scenario of limited resources. Material and methods: In this analytical study, 40 histologically proven unresectable advanced squamous cell carcinoma patients of oropharynx and larynx were allocated in two groups to receive 70 Gy in 35 fractions in 7 weeks with concurrent cisplatinum35 mg/m Results: Plans with best possible coverage of the target volume were obtained. No significant difference was found in the dose received by the spinal cord; however, it was possible to prevent higher dose to brain stem with 3DCRTin node negative patients of oropharynx cancer and larynx cancer. Skin toxicities were significantly lower in 3DCRT arm. Conclusion: In low resource settings with increased burden of locally advanced disease, both open-field and 3DCRT treatment techniques are comparable in terms of target coverage, OARs preservation, toxicity and treatment response.
Language	English
Publishing date	2022-02-01
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2673599-4
ISSN	2251-7200
ISSN	2251-7200
DOI	10.31661/jbpe.v0i0.2007-1132
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Article: Dosimetric Evaluation of Different Optimization Algorithms Used in Interstitial Brachytherapy of Cervical Carcinoma.

Srivastava, Shraddha / Singh, Navin / Kashyap, Varun Kumar

Journal of biomedical physics & engineering

2022 Volume 12, Issue 4, Page(s) 339–348

Abstract: Background: Conventional optimization techniques are based on the planning approach in which positions and weights are varied to generate the desired dose distribution. Inverse planning simulated annealing (IPSA) is an advanced optimization method ... ...

Abstract	Background: Conventional optimization techniques are based on the planning approach in which positions and weights are varied to generate the desired dose distribution. Inverse planning simulated annealing (IPSA) is an advanced optimization method developed to automatically determine a suitable combination of positions to design an acceptable plan. Objective: In this study, three optimization techniques namely IPSA, graphical optimization (GROPT), and geometrical optimization (GOPT) methods are compared in high-dose-rate interstitial brachytherapy of cervical carcinoma. Material and methods: In this retrospective study, twenty computed tomography (CT) data sets of 10 cervical cancer patients treated with Martinez Universal Perineal Interstitial Template-based interstitial brachytherapy were studied. The treatment plans generated were optimized using the IPSA, and GOPT methods. The prescribed dose was 24 Gy in 4 fractions. Plans produced using IPSA, GrOPT, and GOPT techniques were analyzed for comparison of dosimetric parameters, including target coverage, homogeneity, conformity, and organs at risk (OAR) doses. Results: V100 values for IPSA, GrOPT and GOPT plans were 95.81±2.33%, 93.12±2.76% and 88.90±4.95%, respectively. The mean D90 values for the IPSA, GrOPT, and GOPT plans were 6.45±0.15 Gy, 6.12±0.21 Gy, and 5.85±0.57 Gy, respectively. Significantly lower doses of OAR were in the IPSA plans that were more homogeneous (HI=0.66). Conformity was comparatively higher in IPSA-based plans (CI=0.75). Conclusion: IPSA plans were superior and resulted in better target coverage, homogeneity, conformity, and minimal OAR doses.
Language	English
Publishing date	2022-08-01
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2673599-4
ISSN	2251-7200
ISSN	2251-7200
DOI	10.31661/jbpe.v0i0.2104-1306
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Article ; Online: Melting of DNA in confined geometries.

Maity, Arghya / Singh, Navin

European biophysics journal : EBJ

2020 Volume 49, Issue 7, Page(s) 561–569

Abstract: The stability of DNA molecules during viral or biotechnological encapsulation is a topic of active current research. We studied the thermal stability of double-stranded DNA molecules of different lengths in a confined space. Using a statistical model, we ...

Abstract	The stability of DNA molecules during viral or biotechnological encapsulation is a topic of active current research. We studied the thermal stability of double-stranded DNA molecules of different lengths in a confined space. Using a statistical model, we evaluate the melting profile of DNA molecules in two geometries: conical and cylindrical. Our results show that not only the confinement, but also the geometry of the confined space plays a prominent role in the stability and opening of the DNA duplex. We find that for more confined spaces, cylindrical confinement stabilizes the DNA, but for less confined spaces conical geometry stabilizes the DNA overall. We also analyse the interaction between DNA sequence and stability, and the evenness with which strand separation occurs. Cylindrical and conical geometries enable a better controlled tuning of the stability of DNA encapsulation and the efficiency of its eventual release, compared to spherical or quasi-spherical geometries.
MeSH term(s)	Base Sequence ; DNA/chemistry ; DNA/genetics ; Hydrogen Bonding ; Models, Biological ; Nucleic Acid Conformation ; Nucleic Acid Denaturation ; Oligodeoxyribonucleotides/chemical synthesis ; Temperature
Chemical Substances	Oligodeoxyribonucleotides ; DNA (9007-49-2)
Language	English
Publishing date	2020-09-12
Publishing country	Germany
Document type	Journal Article
ZDB-ID	283671-3
ISSN	1432-1017 ; 0175-7571
ISSN (online)	1432-1017
ISSN	0175-7571
DOI	10.1007/s00249-020-01462-9
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Article ; Online: Superiority of a Silk Surgical Site Wound Closure Device Over Synthetic Dressings.

Rouhani, Daniel S / Singh, Navin K / Chao, James J / Almutairi, Adah / Seradj, Mehran H / Badowski-Platz, Rebecca / Toranto, Jason D / Mofid, M Mark

Plastic and reconstructive surgery

2024

Abstract: Background: Silk fibroin is an emerging biomaterial with enhanced properties of cellular regeneration, growth and proliferation. The use of a silk fibroin wound dressing has the potential to decrease the incidence of wound healing complications and to ... ...

Abstract	Background: Silk fibroin is an emerging biomaterial with enhanced properties of cellular regeneration, growth and proliferation. The use of a silk fibroin wound dressing has the potential to decrease the incidence of wound healing complications and to improve patient outcomes compared to synthetic dressing alternatives. Methods: A prospective, randomized, single-blinded clinical trial was conducted on 50 patients who were dressed with a silk fibroin dressing on one side of their body and on the contralateral side with 3M Steri-Strips® after undergoing abdominoplasty, reduction mammaplasty, or brachioplasty procedures. Data was collected over 5 postoperative visits using photographs and an investigator administered questionnaire to monitor erythema, skin irritation, skin discomfort, the need for pharmaceutical intervention, wound dehiscence and mechanical skin injury. A comprehensive 75 patient statistical analysis was conducted combining the results with a previously published study comparing Dermabond® Prineo® to the silk dressing. Results: 20.8% (10/48) of patients were assessed by surgeons as having skin erythema (7-10) on the Steri-Strip® control side and 0% (0/48) on the silk dressing side (p=0.002). The frequency of breast triple point separation in 43 cases was 30.2% (13/43) on the Steri-Strip® side and 9.3% (4/43) on the silk side (p=0.012). 75% (36/48) of patients had partial or total detachment of Steri-Strips® while 0% (0/48) had total detachment of the silk dressing and 18.8% (9/48) had partial detachment of the silk dressing within the first two weeks (p<0.001). Conclusion: A silk fibroin wound dressing significantly reduces the incidence of wound healing complications throughout the postoperative period.Clinical Relevance Statement: The adoption of a silk fibroin wound dressing into clinical practice has the potential to improve patient outcomes, decrease medical adhesive related skin injuries and reduce the rate of wound healing complications.
Language	English
Publishing date	2024-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	208012-6
ISSN	1529-4242 ; 0032-1052 ; 0096-8501
ISSN (online)	1529-4242
ISSN	0032-1052 ; 0096-8501
DOI	10.1097/PRS.0000000000011316
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