PMID-sentid	Pub_year	Sent_text	comp_official_name	comp_offset	protein_name	organism	prot_offset
6438630-1	1984	The Bacillus subtilis phage SP01, whose DNA contains 5-hydroxymethyluracil (hmUra) in place of thymine, codes for an abundant, small, basic protein called TF1.	5-hydroxymethyluracil	53-74	TF1	Bacillus phage SPO1	155-158
2113049-2	1990	3H-Labeled TF1 was allowed to bind to a 32P-labeled DNA fragment containing a TF1 binding site.	Tritium	0-2	TF1	Bacillus phage SPO1	11-14
2113049-2	1990	3H-Labeled TF1 was allowed to bind to a 32P-labeled DNA fragment containing a TF1 binding site.	Tritium	0-2	TF1	Bacillus phage SPO1	78-81
2113049-2	1990	3H-Labeled TF1 was allowed to bind to a 32P-labeled DNA fragment containing a TF1 binding site.	Phosphorus-32	40-43	TF1	Bacillus phage SPO1	11-14
2113049-2	1990	3H-Labeled TF1 was allowed to bind to a 32P-labeled DNA fragment containing a TF1 binding site.	Phosphorus-32	40-43	TF1	Bacillus phage SPO1	78-81
6438630-1	1984	The Bacillus subtilis phage SP01, whose DNA contains 5-hydroxymethyluracil (hmUra) in place of thymine, codes for an abundant, small, basic protein called TF1.	5-hydroxymethyluracil	76-81	TF1	Bacillus phage SPO1	155-158
6438630-1	1984	The Bacillus subtilis phage SP01, whose DNA contains 5-hydroxymethyluracil (hmUra) in place of thymine, codes for an abundant, small, basic protein called TF1.	Thymine	95-102	TF1	Bacillus phage SPO1	155-158
6438630-2	1984	TF1 binds preferentially to hydroxymethyluracil-containing DNA and thereby selectively inhibits transcription of such DNA in vitro.	5-hydroxymethyluracil	28-47	TF1	Bacillus phage SPO1	0-3
12056890-3	2002	TF1, an HU homologue with a 37 bp binding site that is encoded by the Bacillus subtilis bacteriophage SPO1, binds with nM affinity to DNA that contains 5-hydroxymethyluracil (hmU) in place of thymine and to T-containing DNA with loops.	5-hydroxymethyluracil	152-173	TF1	Bacillus phage SPO1	0-3
12873134-4	2003	TF1, an HU homologue that is encoded by Bacillus subtilis bacteriophage SPO1, has nM affinity for 37 bp preferred sites in DNA with 5-hydroxymethyluracil (hmU) in place of thymine.	5-hydroxymethyluracil	132-153	TF1	Bacillus phage SPO1	0-3
12873134-4	2003	TF1, an HU homologue that is encoded by Bacillus subtilis bacteriophage SPO1, has nM affinity for 37 bp preferred sites in DNA with 5-hydroxymethyluracil (hmU) in place of thymine.	5-hydroxymethyluracil	155-158	TF1	Bacillus phage SPO1	0-3
12873134-4	2003	TF1, an HU homologue that is encoded by Bacillus subtilis bacteriophage SPO1, has nM affinity for 37 bp preferred sites in DNA with 5-hydroxymethyluracil (hmU) in place of thymine.	Thymine	172-179	TF1	Bacillus phage SPO1	0-3
12056890-3	2002	TF1, an HU homologue with a 37 bp binding site that is encoded by the Bacillus subtilis bacteriophage SPO1, binds with nM affinity to DNA that contains 5-hydroxymethyluracil (hmU) in place of thymine and to T-containing DNA with loops.	Thymine	192-199	TF1	Bacillus phage SPO1	0-3
12056890-3	2002	TF1, an HU homologue with a 37 bp binding site that is encoded by the Bacillus subtilis bacteriophage SPO1, binds with nM affinity to DNA that contains 5-hydroxymethyluracil (hmU) in place of thymine and to T-containing DNA with loops.	5-hydroxymethyluracil	175-178	TF1	Bacillus phage SPO1	0-3
8764400-0	1996	On the connection between inherent DNA flexure and preferred binding of hydroxymethyluracil-containing DNA by the type II DNA-binding protein TF1.	5-hydroxymethyluracil	72-91	TF1	Bacillus phage SPO1	142-145
9148920-0	1997	Twin hydroxymethyluracil-A base pair steps define the binding site for the DNA-binding protein TF1.	hydroxymethyluracil-a	5-26	TF1	Bacillus phage SPO1	95-98
9148920-2	1997	We recently proposed that TF1, which binds with high affinity (Kd was approximately 3 nM) to preferred sites within the hydroxymethyluracil (hmU)-containing phage genome, identifies its binding sites based on sequence-dependent DNA flexibility.	5-hydroxymethyluracil	120-139	TF1	Bacillus phage SPO1	26-29
9148920-2	1997	We recently proposed that TF1, which binds with high affinity (Kd was approximately 3 nM) to preferred sites within the hydroxymethyluracil (hmU)-containing phage genome, identifies its binding sites based on sequence-dependent DNA flexibility.	5-hydroxymethyluracil	141-144	TF1	Bacillus phage SPO1	26-29
9148920-5	1997	Replacement of all hmU residues with thymine decreases the affinity of TF1 greatly; remarkably, the high affinity is restored when the two hmU-A base pair steps corresponding to previously suggested sites of distortion are reintroduced into otherwise T-containing DNA.	Thymine	37-44	TF1	Bacillus phage SPO1	71-74
8764400-2	1996	Distinctive to TF1, which is encoded by the Bacillus subtilis bacteriophage SPO1, is its preferential binding to DNA in which thymine is replaced by 5-hydroxymethyluracil (hmU), as it is in the phage genome.	Thymine	126-133	TF1	Bacillus phage SPO1	15-18
8764400-2	1996	Distinctive to TF1, which is encoded by the Bacillus subtilis bacteriophage SPO1, is its preferential binding to DNA in which thymine is replaced by 5-hydroxymethyluracil (hmU), as it is in the phage genome.	5-hydroxymethyluracil	149-170	TF1	Bacillus phage SPO1	15-18
8764400-2	1996	Distinctive to TF1, which is encoded by the Bacillus subtilis bacteriophage SPO1, is its preferential binding to DNA in which thymine is replaced by 5-hydroxymethyluracil (hmU), as it is in the phage genome.	5-hydroxymethyluracil	172-175	TF1	Bacillus phage SPO1	15-18
8764400-5	1996	Model flexible sites, consisting of consecutive mismatches, increase the affinity of thymine-containing DNA for TF1.	Thymine	85-92	TF1	Bacillus phage SPO1	112-115
8107099-1	1994	TF1, a homodimeric DNA-binding and -bending protein with a preference for hydroxymethyluracil-containing DNA is the Bacillus subtilis-encoded homolog of the bacterial HU proteins and of the E. coli integration host factor.	5-hydroxymethyluracil	74-93	TF1	Bacillus phage SPO1	0-3
8107099-5	1994	The double mutant protein TF1-G15I32 binds to a preferred site in hydroxymethyluracil-containing DNA 40 times more tightly, denatures at higher temperature (delta tm = 21 degrees C), and also exchanges subunits much more slowly than does the wild-type protein.	5-hydroxymethyluracil	66-85	TF1	Bacillus phage SPO1	26-29
8107099-6	1994	The L25-->A mutation makes TF1 secondary structure and DNA-binding highly salt concentration-dependent.	Salts	77-81	TF1	Bacillus phage SPO1	30-33
8107099-7	1994	The E15-->G mutation partly suppresses this effect: secondary structure of TF1-A25G15 is restored at 21 degrees C by 1 M NaCl or, at low NaCl concentration, by binding to DNA.	Sodium Chloride	124-128	TF1	Bacillus phage SPO1	78-81
8107099-7	1994	The E15-->G mutation partly suppresses this effect: secondary structure of TF1-A25G15 is restored at 21 degrees C by 1 M NaCl or, at low NaCl concentration, by binding to DNA.	Sodium Chloride	140-144	TF1	Bacillus phage SPO1	78-81