Ontology: Molecular Function (GO:0003690)

Definition: Interacting selectively and non-covalently with double-stranded DNA.

Synonyms: dsDNA binding

View Ontology: (graph) | (text)

This table lists the methods used to annotate genes either directly to the term double-stranded DNA binding (31 genes) or to its variants containing one or more qualifiers (6 genes). Note that some genes may have been annotated by more than one method so the numbers in the table below may not add up to the totals given here.

Annotation Method	GO Term	# Yeast Genes Annotated
Manually curated (download data)	contributes_to: double-stranded DNA binding	6
	double-stranded DNA binding	27
High-throughput	none	none
Computational (download data)	double-stranded DNA binding	5

Links to Additional Annotations:

• View annotations in multiple organisms using
• Search for S. cerevisiae genes annotated, by the Manually curated or High-throughput methods, to this term or to any terms that are descended from this term, i.e., child terms representing more specific biology than this term.

Annotation details for genes that have been directly annotated to the term double-stranded DNA binding or its variants containing one or more qualifiers (NOT, contributes to, or colocalizes with).

double-stranded DNA binding      31 genes directly annotated to this term
Locus	Evidence	Annotation Method	Reference	Assigned By
ACO1/YLR304C	IDA: Inferred from Direct Assay Assigned on 2007-08-21	manually curated	Chen XJ, et al.  (2007) Yeast aconitase binds and provides metabolically coupled protection to mitochondrial DNA. Proc Natl Acad Sci U S A 104(34):13738-43	SGD
DMC1/YER179W	IDA: Inferred from Direct Assay Assigned on 2002-05-21	manually curated	Hong EL, et al.  (2001) Saccharomyces cerevisiae Dmc1 protein promotes renaturation of single-strand DNA (ssDNA) and assimilation of ssDNA into homologous super-coiled duplex DNA. J Biol Chem 276(45):41906-12	SGD
FHL1/YPR104C	IBA: Inferred from Biological Aspect of Ancestor with PANTHER:PTHR11829_AN0 Assigned on 2010-04-28	computational	Gaudet P, et al.  (2011) Annotation inferences using phylogenetic trees.	RefGenome
FKH1/YIL131C	IBA: Inferred from Biological Aspect of Ancestor with PANTHER:PTHR11829_AN0 Assigned on 2010-04-28	computational	Gaudet P, et al.  (2011) Annotation inferences using phylogenetic trees.	RefGenome
FKH2/YNL068C	IBA: Inferred from Biological Aspect of Ancestor with PANTHER:PTHR11829_AN0 Assigned on 2010-04-28	computational	Gaudet P, et al.  (2011) Annotation inferences using phylogenetic trees.	RefGenome
FLP1/R0010W	IDA: Inferred from Direct Assay Assigned on 2006-08-04	manually curated	Gronostajski RM and Sadowski PD  (1985) The FLP recombinase of the Saccharomyces cerevisiae 2 microns plasmid attaches covalently to DNA via a phosphotyrosyl linkage. Mol Cell Biol 5(11):3274-9	SGD
HCM1/YCR065W	IBA: Inferred from Biological Aspect of Ancestor with PANTHER:PTHR11829_AN0 Assigned on 2010-04-28	computational	Gaudet P, et al.  (2011) Annotation inferences using phylogenetic trees.	RefGenome
HMO1/YDR174W	IDA: Inferred from Direct Assay Assigned on 2010-03-17	manually curated	Kamau E, et al.  (2004) The Saccharomyces cerevisiae high mobility group box protein HMO1 contains two functional DNA binding domains. J Biol Chem 279(53):55234-40	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-03-17	manually curated	Bauerle KT, et al.  (2006) Interactions between N- and C-terminal domains of the Saccharomyces cerevisiae high-mobility group protein HMO1 are required for DNA bending. Biochemistry 45(11):3635-45	SGD
HOP2/YGL033W	IDA: Inferred from Direct Assay, IPI: Inferred from Physical Interaction Assigned on 2004-10-08	manually curated	Chen YK, et al.  (2004) Heterodimeric complexes of Hop2 and Mnd1 function with Dmc1 to promote meiotic homolog juxtaposition and strand assimilation. Proc Natl Acad Sci U S A 101(29):10572-7	SGD
ILV5/YLR355C	IDA: Inferred from Direct Assay Assigned on 2011-03-31	manually curated	Macierzanka M, et al.  (2008) Maintenance and stabilization of mtDNA can be facilitated by the DNA-binding activity of Ilv5p. Biochim Biophys Acta 1783(1):107-17	SGD
LAP3/YNL239W	IDA: Inferred from Direct Assay Assigned on 2011-06-23	manually curated	Zheng W and Johnston SA  (1998) The nucleic acid binding activity of bleomycin hydrolase is involved in bleomycin detoxification. Mol Cell Biol 18(6):3580-5	SGD
LRP1/YHR081W	IDA: Inferred from Direct Assay Assigned on 2008-10-07	manually curated	Stead JA, et al.  (2007) The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein. Nucleic Acids Res 35(16):5556-67	SGD
MCM10/YIL150C	IDA: Inferred from Direct Assay Assigned on 2009-07-22	manually curated	Eisenberg S, et al.  (2009) Novel DNA Binding Properties of the Mcm10 Protein from Saccharomyces cerevisiae. J Biol Chem 284(37):25412-20	SGD
MND1/YGL183C	IDA: Inferred from Direct Assay, IPI: Inferred from Physical Interaction Assigned on 2004-10-08	manually curated	Chen YK, et al.  (2004) Heterodimeric complexes of Hop2 and Mnd1 function with Dmc1 to promote meiotic homolog juxtaposition and strand assimilation. Proc Natl Acad Sci U S A 101(29):10572-7	SGD
POL2/YNL262W	IDA: Inferred from Direct Assay Assigned on 2012-09-21	manually curated	Tsubota T, et al.  (2003) Double-stranded DNA binding properties of Saccharomyces cerevisiae DNA polymerase epsilon and of the Dpb3p-Dpb4p subassembly. Genes Cells 8(11):873-88	SGD
RAD17/YOR368W	IDA: Inferred from Direct Assay Assigned on 2004-09-29	manually curated	Majka J and Burgers PM  (2003) Yeast Rad17/Mec3/Ddc1: a sliding clamp for the DNA damage checkpoint. Proc Natl Acad Sci U S A 100(5):2249-54	SGD
	IEA: Inferred from Electronic Annotation with EBI:IPR016587 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
RAD50/YNL250W	IDA: Inferred from Direct Assay, IPI: Inferred from Physical Interaction Assigned on 2002-09-25	manually curated	Raymond WE and Kleckner N  (1993) RAD50 protein of S.cerevisiae exhibits ATP-dependent DNA binding. Nucleic Acids Res 21(16):3851-6	SGD
RAD9/YDR217C	IDA: Inferred from Direct Assay Assigned on 2008-10-21	manually curated	Lancelot N, et al.  (2007) The checkpoint Saccharomyces cerevisiae Rad9 protein contains a tandem tudor domain that recognizes DNA. Nucleic Acids Res 35(17):5898-912	SGD
RFA1/YAR007C	IDA: Inferred from Direct Assay Assigned on 2007-09-18	manually curated	Singh KK and Samson L  (1995) Replication protein A binds to regulatory elements in yeast DNA repair and DNA metabolism genes. Proc Natl Acad Sci U S A 92(11):4907-11	SGD
RFA2/YNL312W	IDA: Inferred from Direct Assay Assigned on 2007-09-18	manually curated	Singh KK and Samson L  (1995) Replication protein A binds to regulatory elements in yeast DNA repair and DNA metabolism genes. Proc Natl Acad Sci U S A 92(11):4907-11	SGD
RFA3/YJL173C	IDA: Inferred from Direct Assay Assigned on 2007-09-18	manually curated	Singh KK and Samson L  (1995) Replication protein A binds to regulatory elements in yeast DNA repair and DNA metabolism genes. Proc Natl Acad Sci U S A 92(11):4907-11	SGD
RTT106/YNL206C	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2011-12-12	manually curated	Liu Y, et al.  (2010) Structural analysis of Rtt106p reveals a DNA binding role required for heterochromatin silencing. J Biol Chem 285(6):4251-62	SGD
SAE2/YGL175C	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2008-05-01	manually curated	Lengsfeld BM, et al.  (2007) Sae2 Is an Endonuclease that Processes Hairpin DNA Cooperatively with the Mre11/Rad50/Xrs2 Complex. Mol Cell 28(4):638-51	SGD
SIR3/YLR442C	IDA: Inferred from Direct Assay Assigned on 2009-03-11	manually curated	Adkins NL, et al.  (2009) Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers. Biochemistry 48(2):276-88	SGD
SIR4/YDR227W	IDA: Inferred from Direct Assay Assigned on 2009-03-03	manually curated	Martino F, et al.  (2009) Reconstitution of yeast silent chromatin: multiple contact sites and O-AADPR binding load SIR complexes onto nucleosomes in vitro. Mol Cell 33(3):323-34	SGD
SMC1/YFL008W	IDA: Inferred from Direct Assay Assigned on 2001-01-18	manually curated	Akhmedov AT, et al.  (1998) Structural maintenance of chromosomes protein C-terminal domains bind preferentially to DNA with secondary structure. J Biol Chem 273(37):24088-94	SGD
SMC2/YFR031C	IDA: Inferred from Direct Assay Assigned on 2001-01-18	manually curated	Akhmedov AT, et al.  (1998) Structural maintenance of chromosomes protein C-terminal domains bind preferentially to DNA with secondary structure. J Biol Chem 273(37):24088-94	SGD
TFB2/YPL122C	IDA: Inferred from Direct Assay Assigned on 2010-06-01	manually curated	Kainov DE, et al.  (2010) Interacting partners of the Tfb2 subunit from yeast TFIIH. DNA Repair (Amst) 9(1):33-39	SGD
THO1/YER063W	IDA: Inferred from Direct Assay Assigned on 2007-07-31	manually curated	Jimeno S, et al.  (2006) Tho1, a novel hnRNP, and Sub2 provide alternative pathways for mRNP biogenesis in yeast THO mutants. Mol Cell Biol 26(12):4387-98	SGD
THP1/YOL072W	IDA: Inferred from Direct Assay Assigned on 2009-07-27	manually curated	Gallardo M, et al.  (2003) Nab2p and the Thp1p-Sac3p complex functionally interact at the interface between transcription and mRNA metabolism. J Biol Chem 278(26):24225-32	SGD

contributes_to: double-stranded DNA binding      6 genes directly annotated to this term
Locus	Evidence	Annotation Method	Reference	Assigned By
DPB2/YPR175W	IDA: Inferred from Direct Assay Assigned on 2012-09-21	manually curated	Tsubota T, et al.  (2003) Double-stranded DNA binding properties of Saccharomyces cerevisiae DNA polymerase epsilon and of the Dpb3p-Dpb4p subassembly. Genes Cells 8(11):873-88	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-03-10	manually curated	Tsubota T, et al.  (2006) Double-stranded DNA Binding, an Unusual Property of DNA Polymerase {epsilon}, Promotes Epigenetic Silencing in Saccharomyces cerevisiae. J Biol Chem 281(43):32898-908	SGD
DPB3/YBR278W	IDA: Inferred from Direct Assay Assigned on 2012-09-21	manually curated	Tsubota T, et al.  (2003) Double-stranded DNA binding properties of Saccharomyces cerevisiae DNA polymerase epsilon and of the Dpb3p-Dpb4p subassembly. Genes Cells 8(11):873-88	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-03-10	manually curated	Tsubota T, et al.  (2006) Double-stranded DNA Binding, an Unusual Property of DNA Polymerase {epsilon}, Promotes Epigenetic Silencing in Saccharomyces cerevisiae. J Biol Chem 281(43):32898-908	SGD
DPB4/YDR121W	IDA: Inferred from Direct Assay Assigned on 2012-09-21	manually curated	Tsubota T, et al.  (2003) Double-stranded DNA binding properties of Saccharomyces cerevisiae DNA polymerase epsilon and of the Dpb3p-Dpb4p subassembly. Genes Cells 8(11):873-88	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-03-10	manually curated	Tsubota T, et al.  (2006) Double-stranded DNA Binding, an Unusual Property of DNA Polymerase {epsilon}, Promotes Epigenetic Silencing in Saccharomyces cerevisiae. J Biol Chem 281(43):32898-908	SGD
MLH1/YMR167W	IDA: Inferred from Direct Assay Assigned on 2007-04-06	manually curated	Hall MC, et al.  (2001) High affinity cooperative DNA binding by the yeast Mlh1-Pms1 heterodimer. J Mol Biol 312(4):637-47	SGD
PMS1/YNL082W	IDA: Inferred from Direct Assay Assigned on 2007-04-06	manually curated	Hall MC, et al.  (2001) High affinity cooperative DNA binding by the yeast Mlh1-Pms1 heterodimer. J Mol Biol 312(4):637-47	SGD
POL2/YNL262W	IDA: Inferred from Direct Assay Assigned on 2009-03-10	manually curated	Tsubota T, et al.  (2006) Double-stranded DNA Binding, an Unusual Property of DNA Polymerase {epsilon}, Promotes Epigenetic Silencing in Saccharomyces cerevisiae. J Biol Chem 281(43):32898-908	SGD

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