Nucleic Acids

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Distance

DD, DIS, MDIS, MDISG, ODIS, OPOS, OPOS2, ORAD, ORAD2, POS, RAD

Angle

ANG, ANG2, AXANG, AXANG2, DIH, DIH2, PANG, PVANG

Coordination

CNFF, CNGFF, CNSW, CNGSW, CNRF, CNGRF

Shape

ACYL, ASPH, EVEC, PMGTD, PMOGT, PLANE, RGYR, RMSDT, SANIS

Nucleic Acids

NALBPP, NASBPP, NASBPPOLD, NALSTP, NASSTP, NASSTPOLD, NASBO, NAPBO, NABEND

Puckering

PUCK6Q, PUCK6P, PUCK6T, PUCK5Q, PUCK5P

Special

WORMPOS, WORMANG

Energy

POT, EGAP

Algebra

ADD, SUB, MULT, DIV, FSWITCH, RSWITCH

Collective Variables For Nucleic Acids

Type	Description
NALBPP	local base-pair parameters
NASBPP	simple base-pair parameters
NASBPPOLD	simple base-pair parameters (OLD implementation)
NALSTP	local base-pair step parameters
NASSTP	simple base-pair step parameters
NASSTPOLD	simple base-pair step parameters (OLD implementation)
NASBO	simple base-pair opening
NAPBO	primitive base-pair opening
NABEND	nucleic acid bending

Base-Pair Parameters

PMFLib offers two variants of the base-pair parameters, local and simple, which both are fully compatible with 3DNA. They differ in the definition of the y-axis and the procedure to calculate six base-pair parameters, i.e., Shear, Stretch, Stagger, Buckle, Propeller, Opening.

The simple version is provided by NASBPP. It uses an explicitly defined y-axis and Buckle, Propeller, Opening parameters are calculated as dihedral angles.

The local version is provided by NALBPP. It uses a y-axis derived from the superimposed reference frames of two nucleobases and all parameters are calculated using the CEHS scheme.

The collective variable NASBO implements simple Opening only and thus it should be a little bit computationally faster than NASBPP.

Base-Pair Step Parameters

PMFLib offers two variants of the base-pair step parameters, local and simple, which both are fully compatible with 3DNA. They differ in the definition of the y-axes, i.e., Shift, Slide, Rise, Tilt, Roll, Twist.

The simple version is provided by NASSTP. It uses explicitly defined y-axes of two base pairs and all parameters are calculated using the CEHS scheme.

The local version is provided by NALSTP. It uses y-axes derived from the superimposed reference frames of four nucleobases and all parameters are calculated using the CEHS scheme.

Reference Frames of Nucleobases

Reference coordinates for nucleobase rings are provided in the following table:

Nucleobase	Ring Atoms	y-axis (BPP)	y-axis (STP)	File
A	@N9,C8,N7,C5,C6,N1,C2,N3,C4	@C8	@C1'	A_ring_only.xyz
G	@N9,C8,N7,C5,C6,N1,C2,N3,C4	@C8	@C1'	G_ring_only.xyz
C	@N1,C6,C5,C4,N3,C2	@C6	@C1'	C_ring_only.xyz
T	@N1,C6,C5,C4,N3,C2	@C6	@C1'	T_ring_only.xyz

References

• Applications
  • Bouchal, T.; Durník, I.; Illík, V.; Réblová, K.; Kulhánek, P. Importance of Base-Pair Opening for Mismatch Recognition. Nucleic Acids Res. 2020, 48 (20), 11322–11334. https://doi.org/10.1093/nar/gkaa896.
  • Ruzicka, M.; Soucek, R.; Kulhanek, P.; Radova, L.; Fajkusova, L.; Reblova, K. Bending of DNA Duplexes with Mutation Motifs. DNA Res. 2019, 26 (4), 341–352. https://doi.org/10.1093/dnares/dsz013.
  • Spackova, N.; Reblova, K. Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes. Genes 2018, 9 (7), 324. https://doi.org/10.3390/genes9070324.
  • Ruzicka, M.; Kulhanek, P.; Radova, L.; Cechova, A.; Spackova, N.; Fajkusova, L.; Reblova, K. DNA Mutation Motifs in the Genes Associated with Inherited Diseases. PLOS ONE 2017, 12 (8), e0182377. https://doi.org/10.1371/journal.pone.0182377.
• CEHS Scheme
  • Lu, X. J.; ElHassan, M. A.; Hunter, C. A. Structure and Conformation of Helical Nucleic Acids: Analysis Program (SCHNAaP). J. Mol. Biol. 1997, 273 (3), 668–680. https://doi.org/10.1006/jmbi.1997.1346.
• 3DNA
  • Lu, X.-J.; Olson, W. K. 3DNA: A Versatile, Integrated Software System for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic-Acid Structures. Nature Protocols 2008, 3 (7), 1213–1227. https://doi.org/10.1038/nprot.2008.104.
  • Lu, X.-J.; Olson, W. K. 3DNA: A Software Package for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic Acid Structures. Nucl. Acids Res. 2003, 31 (17), 5108–5121. https://doi.org/10.1093/nar/gkg680.
• Gradients
  • Blanc, E.; Paciorek, W. On Planarity and Similarity Restraints. J. Appl. Crystallogr. 2001, 34, 480–483. https://doi.org/10.1107/S0021889801008470.