PMID- 32406923
OWN - NLM
STAT- MEDLINE
DCOM- 20200908
LR  - 20240329
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Print)
IS  - 0305-1048 (Linking)
VI  - 48
IP  - 11
DP  - 2020 Jun 19
TI  - A unified dinucleotide alphabet describing both RNA and DNA structures.
PG  - 6367-6381
LID - 10.1093/nar/gkaa383 [doi]
AB  - By analyzing almost 120 000 dinucleotides in over 2000 nonredundant nucleic acid 
      crystal structures, we define 96+1 diNucleotide Conformers, NtCs, which describe 
      the geometry of RNA and DNA dinucleotides. NtC classes are grouped into 15 codes 
      of the structural alphabet CANA (Conformational Alphabet of Nucleic Acids) to 
      simplify symbolic annotation of the prominent structural features of NAs and 
      their intuitive graphical display. The search for nontrivial patterns of NtCs 
      resulted in the identification of several types of RNA loops, some of them 
      observed for the first time. Over 30% of the nearly six million dinucleotides in 
      the PDB cannot be assigned to any NtC class but we demonstrate that up to a half 
      of them can be re-refined with the help of proper refinement targets. A 
      statistical analysis of the preferences of NtCs and CANA codes for the 16 
      dinucleotide sequences showed that neither the NtC class AA00, which forms the 
      scaffold of RNA structures, nor BB00, the DNA most populated class, are sequence 
      neutral but their distributions are significantly biased. The reported automated 
      assignment of the NtC classes and CANA codes available at dnatco.org provides a 
      powerful tool for unbiased analysis of nucleic acid structures by structural and 
      molecular biologists.
CI  - © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic 
      Acids Research.
FAU - Černý, Jiří
AU  - Černý J
AD  - Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, CZ-252 50 
      Vestec, Prague-West, Czech Republic.
FAU - Božíková, Paulína
AU  - Božíková P
AD  - Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, CZ-252 50 
      Vestec, Prague-West, Czech Republic.
FAU - Svoboda, Jakub
AU  - Svoboda J
AD  - Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, CZ-252 50 
      Vestec, Prague-West, Czech Republic.
FAU - Schneider, Bohdan
AU  - Schneider B
AD  - Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, CZ-252 50 
      Vestec, Prague-West, Czech Republic.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
RN  - 0 (Nucleotides)
RN  - 0 (RNA, Catalytic)
RN  - 0 (Riboswitch)
RN  - 63231-63-0 (RNA)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - Binding Sites
MH  - Biocatalysis
MH  - DNA/*chemistry/*classification
MH  - *Nucleic Acid Conformation
MH  - *Nucleotide Motifs
MH  - Nucleotides/*chemistry/*classification
MH  - RNA/*chemistry/*classification
MH  - RNA, Catalytic/chemistry/metabolism
MH  - Reproducibility of Results
MH  - Ribosomes/chemistry/metabolism
MH  - Riboswitch
PMC - PMC7293047
EDAT- 2020/05/15 06:00
MHDA- 2020/09/09 06:00
PMCR- 2020/05/14
CRDT- 2020/05/15 06:00
PHST- 2020/04/30 00:00 [accepted]
PHST- 2020/04/11 00:00 [revised]
PHST- 2020/04/11 00:00 [received]
PHST- 2020/05/15 06:00 [pubmed]
PHST- 2020/09/09 06:00 [medline]
PHST- 2020/05/15 06:00 [entrez]
PHST- 2020/05/14 00:00 [pmc-release]
AID - 5837055 [pii]
AID - gkaa383 [pii]
AID - 10.1093/nar/gkaa383 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 2020 Jun 19;48(11):6367-6381. doi: 10.1093/nar/gkaa383.
