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Yadav H, Algaonkar PS, Chakraborty S, Ramakrishna W. Combing of picogram level DNA equivalent to genomic DNA present in single human cell by self propelled droplet motion over a stable gradient surface. J Colloid Interface Sci 2024; 655:451-465. [PMID: 37951002 DOI: 10.1016/j.jcis.2023.11.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/22/2023] [Accepted: 11/05/2023] [Indexed: 11/13/2023]
Abstract
DNA combing is a powerful technique for studying replication profile, fork-directionality and fork velocity. At present, there is requirement of a methodology to comb DNA present in a single human cell for studying replication dynamics at early embryonic stage. In our study, a surface having dual characteristics i.e., affinity towards negatively charged single DNA molecules and a hydrophobic gradient for self propelled droplet motion of combing solution was developed. The surface was made by coating of TCOS (trichloro-octylsilane) by vapor diffusion on APTES (Aminopropyl-triethoxysilane) coated glass slides. A gradient surface having high deposition efficiency (DE) was developed on which 5 picogram DNA equivalent to genomic DNA present in one single human cell can be combed. The gradient surface was thermostable in nature having the ability to sustain boiling temperature for two hours and sustain anisotropy in 70 % ethanol for 80 h. Applicability for multiple runs was enhanced such that the surface can be used for 13-14 times. Factors associated with gradient surface are unidirectional movement of combing solution droplet over the gradient surface for combing straight DNA molecules and a longer gradient surface of more than 1 cm such that long size DNA molecules can be combed. Ellipsometry and contact angle hysteresis confirmed the presence of hydrophobic gradient. XPS (X-ray photoelectron spectroscopy) and FTIR (Fourier Transform Infrared Spectroscopy) confirmed the presence of characteristic affinity towards negatively charged DNA molecules on the gradient surface. Combing solution was optimized for increasing deposition efficiency and for increasing the applicability of gradient surface for multiple runs. High temperature of combing solution was found to increase Deposition Efficiency. Combing solution was also optimized for combing single DNA molecules over the gradient surface. Single DNA molecules were combed by reducing pH and lowering concentration of triton-X in the combing solution. Dye: bp ratio was optimized for high fluorescent intensity and low surface background.
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Affiliation(s)
- Hemendra Yadav
- Department of Biochemistry, Central University of Punjab, Ghudda, India.
| | | | - Sudip Chakraborty
- Department of Computational Sciences, Central University of Punjab, Ghudda, India
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Vervoort L, Demaerel W, Rengifo LY, Odrzywolski A, Vergaelen E, Hestand MS, Breckpot J, Devriendt K, Swillen A, McDonald-McGinn DM, Fiksinski AM, Zinkstok JR, Morrow BE, Heung T, Vorstman JAS, Bassett AS, Chow EWC, Shashi V, Vermeesch JR. Atypical chromosome 22q11.2 deletions are complex rearrangements and have different mechanistic origins. Hum Mol Genet 2019; 28:3724-3733. [PMID: 31884517 PMCID: PMC6935389 DOI: 10.1093/hmg/ddz166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 11/13/2022] Open
Abstract
The majority (99%) of individuals with 22q11.2 deletion syndrome (22q11.2DS) have a deletion that is caused by non-allelic homologous recombination between two of four low copy repeat clusters on chromosome 22q11.2 (LCR22s). However, in a small subset of patients, atypical deletions are observed with at least one deletion breakpoint within unique sequence between the LCR22s. The position of the chromosome breakpoints and the mechanisms driving those atypical deletions remain poorly studied. Our large-scale, whole genome sequencing study of >1500 subjects with 22q11.2DS identified six unrelated individuals with atypical deletions of different types. Using a combination of whole genome sequencing data and fiber-fluorescence in situ hybridization, we mapped the rearranged alleles in these subjects. In four of them, the distal breakpoints mapped within one of the LCR22s and we found that the deletions likely occurred by replication-based mechanisms. Interestingly, in two of them, an inversion probably preceded inter-chromosomal 'allelic' homologous recombination between differently oriented LCR22-D alleles. Inversion associated allelic homologous recombination (AHR) may well be a common mechanism driving (atypical) deletions on 22q11.2.
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Affiliation(s)
| | | | | | - Adrian Odrzywolski
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Elfi Vergaelen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Matthew S Hestand
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | | | - Koen Devriendt
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ann Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ania M Fiksinski
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- The Dalglish Family 22q Clinic and Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Janneke R Zinkstok
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tracy Heung
- The Dalglish Family 22q Clinic and Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Jacob A S Vorstman
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- The Dalglish Family 22q Clinic and Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Anne S Bassett
- The Dalglish Family 22q Clinic and Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Eva W C Chow
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Clinical Genetics Service, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Vandana Shashi
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
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