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Ascona B-DNA Consortium

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The Ascona B-DNA Consortium (ABC) is a collaborative international research initiative founded in 2001 to investigate the sequence-dependent mechanical properties of DNA using molecular dynamics (MD) simulations. The consortium has contributed significantly to the understanding of DNA structure and dynamics over the past two decades, from the atomic level to larger chromatin structures. The ABC's work includes the development of simulation standards, force fields, and data libraries for DNA, enabling the systematic study of sequence effects across different nucleotide configurations.

History

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The ABC was founded in 2001 during an informal meeting led by a group of scientist that was attending to the "Atomistic to Continuum Models for Long Molecules" conference in Ascona, Switzerland. The consortium started by joining efforts from nine laboratories with expertise in DNA molecular dynamics and sequence-dependent DNA effects.[1] The initial aim was to conduct state-of-the-art MD simulations to establish standards for DNA modeling and to analyze the effects of sequence on DNA's structure and flexibility.[1]

Phase I and II

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In its initial phase, known as Phase I (2004–2005), the ABC conducted 15-nanosecond simulations of 10 different 15-mer DNA sequences using the parm94[2] force field. This study, which analyzed sequence effects at the dinucleotide level, marked the first systematic approach to DNA simulation in the field.[3][4]

Following improvements in force fields, the consortium launched Phase II between 2007 and 2009, re-running the initial simulations using the parmbsc0[5] force field (developed at the Barcelona Supercomputing Center) and extending simulation times to 50 nanoseconds for a set of 39 DNA sequences. This phase allowed the first comprehensive study of all 136 unique tetranucleotide combinations.[6]

µABC, miniABC, and hexABC

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To address limitations in simulation times, the µABC project (2010–2014) pushed simulations into the microsecond range with 39 B-DNA 18-mer sequences containing at least 3 copies of all the unique tetranucleotides, facilitating studies of convergence.[7] Results from this study were key in leading to the creation of the parmbsc1[8] force field, a state-of-the-art set of parameters for the simulation of DNA alone or in complex with other biomolecules. Using this refined force field a project known as miniABC, involved simulations of a minimal library of 13 B-DNA sequences under diverse salt conditions, which enabled further analysis of tetranucleotides and allowed the extension and refinment of Calladine–Dickerson rules[9][10] including subtle conformational polymorphisms of DNA structure.[11]

Currently, the hexABC project seeks to advance DNA conformational studies by simulating 950 20-mer sequences over the sub-millisecond timescale. This project aims to investigate the effects of next-to-nearest neighbor interactions, covering all 2080 unique hexanucleotide combinations with the latest force fields parmbsc1 and OL15.[12] HexABC is the joint effort of 14 research institutions: EPFL Lausanne, Kaunas University of Technology, Gdańsk University of Technology, IRB Barcelona, Jülich Supercomputing Center, Louisiana Tech University, University of Cambridge, University of Florida, University of Leeds, University of Nottingham, University of the Republic of Uruguay, University of Utah, University of York and ENS Paris-Saclay.[13]

2023 meeting

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Special issue devoted to the 2023 ABC meeting
Participants of the ABC meeting
Participants of the ABC meeting held in Ascona (Switzerland) from 17-21 April 2023.

In April 2023, the ABC celebrated its 22nd anniversary by hosting a conference back in Ascona, Switzerland. This event brought together consortium members and collaborators to discuss recent theoretical and experimental developments in DNA structure and dynamics, including sequence effects on DNA interactions within chromatin. [14]

The conference, funded by the Centre Européen de Calcul Atomique et Moléculaire and the Congressi Stefano Francini, featured three keynote presentations, 39 oral communications, and two poster sessions.[14]

A special issue of the Biophysical Reviews journal edited by Prof Wilma Olson and published by Springer Nature was devoted to some of the studies presented at the conference.[15]

Current members

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The current members of the ABC consortium, as of 2024, are active contributors to the consortium's ongoing projects:[13]

References

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  1. ^ a b Beveridge, David L.; Cheatham, Thomas E.; Mezei, Mihaly (2012-07-01). "The ABCs of molecular dynamics simulations on B-DNA, circa 2012". Journal of Biosciences. 37 (3): 379–397. doi:10.1007/s12038-012-9222-6. ISSN 0973-7138. PMC 4029509. PMID 22750978.
  2. ^ Cornell, Wendy D.; Cieplak, Piotr; Bayly, Christopher I.; Gould, Ian R.; Merz, Kenneth M.; Ferguson, David M.; Spellmeyer, David C.; Fox, Thomas; Caldwell, James W.; Kollman, Peter A. (May 1995). "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules". Journal of the American Chemical Society. 117 (19): 5179–5197. Bibcode:1995JAChS.117.5179C. doi:10.1021/ja00124a002. ISSN 0002-7863.
  3. ^ Beveridge, David L.; Barreiro, Gabriela; Suzie Byun, K.; Case, David A.; Cheatham, Thomas E.; Dixit, Surjit B.; Giudice, Emmanuel; Lankas, Filip; Lavery, Richard; Maddocks, John H.; Osman, Roman; Seibert, Eleanore; Sklenar, Heinz; Stoll, Gautier; Thayer, Kelly M. (December 2004). "Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(CpG) Steps". Biophysical Journal. 87 (6): 3799–3813. Bibcode:2004BpJ....87.3799B. doi:10.1529/biophysj.104.045252. PMC 1304892. PMID 15326025.
  4. ^ Dixit, Surjit B.; Beveridge, David L.; Case, David A.; Cheatham, Thomas E.; Giudice, Emmanuel; Lankas, Filip; Lavery, Richard; Maddocks, John H.; Osman, Roman; Sklenar, Heinz; Thayer, Kelly M.; Varnai, Péter (December 2005). "Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps". Biophysical Journal. 89 (6): 3721–3740. Bibcode:2005BpJ....89.3721D. doi:10.1529/biophysj.105.067397. ISSN 0006-3495. PMC 1366942. PMID 16169978.
  5. ^ Pérez, Alberto; Marchán, Iván; Svozil, Daniel; Sponer, Jiri; Cheatham, Thomas E.; Laughton, Charles A.; Orozco, Modesto (June 2007). "Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers". Biophysical Journal. 92 (11): 3817–3829. Bibcode:2007BpJ....92.3817P. doi:10.1529/biophysj.106.097782. ISSN 0006-3495. PMC 1868997. PMID 17351000.
  6. ^ Lavery, Richard; Zakrzewska, Krystyna; Beveridge, David; Bishop, Thomas C.; Case, David A.; Cheatham, Thomas; Dixit, Surjit; Jayaram, B.; Lankas, Filip; Laughton, Charles; Maddocks, John H.; Michon, Alexis; Osman, Roman; Orozco, Modesto; Perez, Alberto (2009-11-06). "A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA". Nucleic Acids Research. 38 (1): 299–313. doi:10.1093/nar/gkp834. ISSN 0305-1048. PMC 2800215. PMID 19850719.
  7. ^ Pasi, Marco; Maddocks, John H.; Beveridge, David; Bishop, Thomas C.; Case, David A.; Cheatham, Thomas; Dans, Pablo D.; Jayaram, B.; Lankas, Filip; Laughton, Charles; Mitchell, Jonathan; Osman, Roman; Orozco, Modesto; Pérez, Alberto; Petkevičiūtė, Daiva (2014-09-26). "μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA". Nucleic Acids Research. 42 (19): 12272–12283. doi:10.1093/nar/gku855. ISSN 1362-4962. PMC 4231739. PMID 25260586.
  8. ^ Ivani, Ivan; Dans, Pablo D.; Noy, Agnes; Pérez, Alberto; Faustino, Ignacio; Hospital, Adam; Walther, Jürgen; Andrio, Pau; Goñi, Ramon; Balaceanu, Alexandra; Portella, Guillem; Battistini, Federica; Gelpí, Josep Lluis; González, Carlos; Vendruscolo, Michele (January 2016). "Parmbsc1: a refined force field for DNA simulations". Nature Methods. 13 (1): 55–58. doi:10.1038/nmeth.3658. ISSN 1548-7105. PMC 4700514. PMID 26569599.
  9. ^ Dickerson, Richard E.; Klug, A. (1983-05-25). "Base sequence and helix structure variation in B and A DNA". Journal of Molecular Biology. 166 (3): 419–441. doi:10.1016/S0022-2836(83)80093-X. ISSN 0022-2836. PMID 6854650.
  10. ^ Calladine, C. R. (2004). Understanding DNA: the molecule & how it works (3rd ed.). San Diego, CA: Elsevier Academic Press. ISBN 978-0-12-155089-9.
  11. ^ Dans, Pablo D; Balaceanu, Alexandra; Pasi, Marco; Patelli, Alessandro S; Petkevičiūtė, Daiva; Walther, Jürgen; Hospital, Adam; Bayarri, Genís; Lavery, Richard; Maddocks, John H; Orozco, Modesto (2019-10-18). "The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules". Nucleic Acids Research. 47 (21): 11090–11102. doi:10.1093/nar/gkz905. ISSN 0305-1048. PMC 6868377. PMID 31624840.
  12. ^ Zgarbová, Marie; Šponer, Jiří; Otyepka, Michal; Cheatham, Thomas E.; Galindo-Murillo, Rodrigo; Jurečka, Petr (2015-12-08). "Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA". Journal of Chemical Theory and Computation. 11 (12): 5723–5736. doi:10.1021/acs.jctc.5b00716. ISSN 1549-9618. PMID 26588601.
  13. ^ a b "hexABC project". IRB Barcelona. 11/5/2024. Retrieved 11/5/2024
  14. ^ a b Dans, Pablo (2024-06-01). "Multiscale simulations of DNA from electrons to nucleosomes: 22 years of the Ascona B-DNA Consortium". Biophysical Reviews. 16 (3): 265–267. doi:10.1007/s12551-024-01194-6. ISSN 1867-2469. PMC 11296982. PMID 39099842.
  15. ^ "Biophysical Reviews | Volume 16, issue 3". 2024.
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