Creating mismatched DNA duplex using NAB - Revision history

Nn320 at 11:01, 30 January 2020

2020-01-30T11:01:04Z

← Older revision		Revision as of 11:01, 30 January 2020
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	*Paste these two parts one after the other into a new pdb file TGmismatch.pdb		*Paste these two parts one after the other into a new pdb file TGmismatch.pdb
	However there is a problem! The atom numbers as found in column 2 of TGmismatch.pdb are not in correct order.		However there is a problem! The atom numbers as found in column 2 of TGmismatch.pdb are not in correct order.
			=====Correcting pdb file=====
	*To correct atom numbers, simply go to the end of file, and generate numbers from 381 to 761 using the following Ex command in vim		*To correct atom numbers, simply go to the end of file, and generate numbers from 381 to 761 using the following Ex command in vim
	<pre>		<pre>
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	*Now, simply use <b>Ctrl+V</b>, <b>x </b>and <b>Esc </b>to delete the column containing incorrect atom numbers and also for modifying the spacing between columns in pdb file.		*Now, simply use <b>Ctrl+V</b>, <b>x </b>and <b>Esc </b>to delete the column containing incorrect atom numbers and also for modifying the spacing between columns in pdb file.
	*Make sure the last line of the TGmismatch.pdb file (i.e. line number 763 here) is <b>TER</b>. 'TER' is used to separate parts of pdb file which are not connected covalently. In our pdb file 'TER' occurs twice.		*Make sure the last line of the TGmismatch.pdb file (i.e. line number 763 here) is <b>TER</b>. 'TER' is used to separate parts of pdb file which are not connected covalently. In our pdb file 'TER' occurs twice.
			*<b>Alternatively</b> we can also use pdb4amber command in ambertools (this shortcut method needs to be checked, not sure about it!)
			<pre>
			pdb4amber -i TGmismatch.pdb -o TGmismatch_for_amber.pdb
			</pre>
			In case, we don't want Hydrogen atoms in our pdb file for use with leap, add --nohyd i.e.
			<pre>
			pdb4amber -i TGmismatch.pdb -o TGmismatch_for_amber.pdb --nohyd
			</pre>
	Our pdb file containing the mismatched TG base pair is ready to be viewed using vmd :)		Our pdb file containing the mismatched TG base pair is ready to be viewed using vmd :)

Nn320 at 10:35, 30 January 2020

2020-01-30T10:35:19Z

← Older revision		Revision as of 10:35, 30 January 2020
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	*Go to line number 382 of TGmismatch.pdb, place cursor next to column two and use <b>p</b> command to paste the yanked column.		*Go to line number 382 of TGmismatch.pdb, place cursor next to column two and use <b>p</b> command to paste the yanked column.
	*Now, simply use <b>Ctrl+V</b>, <b>x </b>and <b>Esc </b>to delete the column containing incorrect atom numbers and also for modifying the spacing between columns in pdb file.		*Now, simply use <b>Ctrl+V</b>, <b>x </b>and <b>Esc </b>to delete the column containing incorrect atom numbers and also for modifying the spacing between columns in pdb file.
	*Make sure the last line of the TGmismatch.pdb file (i.e. line number 763 here) is <b>TER</b>		*Make sure the last line of the TGmismatch.pdb file (i.e. line number 763 here) is <b>TER</b>. 'TER' is used to separate parts of pdb file which are not connected covalently. In our pdb file 'TER' occurs twice.
	Our pdb file containing the mismatched TG base pair is ready to be viewed using vmd :)		Our pdb file containing the mismatched TG base pair is ready to be viewed using vmd :)

Nn320 at 09:42, 30 January 2020

2020-01-30T09:42:52Z

← Older revision		Revision as of 09:42, 30 January 2020
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	module load ambertools/16/19		module load ambertools/16/19
	module load mpi/openmpi/64/gnu/1.6.5		module load mpi/openmpi/64/gnu/1.6.5
			module load amber/14
	</pre>		</pre>
	Create input files for both strands. Note that input file must end with <b>.nab</b>		Create input files for both strands. Note that input file must end with <b>.nab</b>

Nn320: /* Merging pdb files */

2020-01-30T09:05:13Z

Merging pdb files

← Older revision		Revision as of 09:05, 30 January 2020
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	*Take the lines starting from 380 to 761 from strand2.pdb. This corresponds to 3'-5' strand that we want.		*Take the lines starting from 380 to 761 from strand2.pdb. This corresponds to 3'-5' strand that we want.
	*Paste these two parts one after the other into a new pdb file TGmismatch.pdb		*Paste these two parts one after the other into a new pdb file TGmismatch.pdb
	However there is a problem! The atom numbers as found in column 2 of pdb ~~have~~ ~~changed~~.		However there is a problem! The atom numbers as found in column 2 of TGmismatch.pdb are not in correct order.
	*To correct atom numbers, simply go to the end of file, and generate numbers from 381 to 761 using the following Ex command in vim		*To correct atom numbers, simply go to the end of file, and generate numbers from 381 to 761 using the following Ex command in vim
	<pre>		<pre>

Nn320 at 09:02, 30 January 2020

2020-01-30T09:02:25Z

← Older revision		Revision as of 09:02, 30 January 2020
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	As an example let's try to make a DNA duplex containing one TG mismatched base pair i.e. two strands with the following sequence-		As an example let's try to make a DNA duplex containing one TG mismatched base pair i.e. two strands with the following sequence-

	5'-~~GCTCATGACAGG~~-3'		5'-GCTCA<b>T</b>GACAGG-3'

	3'-~~CGAGTGCTGTCC~~-5'		3'-CGAGT<b>G</b>CTGTCC-5'

	===STEPS===		===STEPS===

Nn320 at 18:29, 29 January 2020

2020-01-29T18:29:26Z

← Older revision		Revision as of 18:29, 29 January 2020
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	As an example let's try to make a DNA duplex containing one TG mismatched base pair i.e. two strands with the following sequence-		As an example let's try to make a DNA duplex containing one TG mismatched base pair i.e. two strands with the following sequence-

	5'-GCTCATGACAGG-3'		5'-GCTCATGACAGG-3'

Nn320 at 18:29, 29 January 2020

2020-01-29T18:29:11Z

← Older revision		Revision as of 18:29, 29 January 2020
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	As an example let's try to make a DNA duplex containing one TG mismatched base pair i.e. two strands with the following sequence-		As an example let's try to make a DNA duplex containing one TG mismatched base pair i.e. two strands with the following sequence-
	5'-GCTCATGACAGG-3'		5'-GCTCATGACAGG-3'

	3'-CGAGTGCTGTCC-5'		3'-CGAGTGCTGTCC-5'

Nn320 at 18:28, 29 January 2020

2020-01-29T18:28:51Z

← Older revision		Revision as of 18:28, 29 January 2020
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	As an example let's try to make a DNA duplex containing one TG mismatched base pair i.e. two strands with the following sequence-		As an example let's try to make a DNA duplex containing one TG mismatched base pair i.e. two strands with the following sequence-
	5'-~~GCTCATGACAGA~~-3'		5'-GCTCATGACAGG-3'
	3'-~~CGAGTGCTGTCT~~-5'		3'-CGAGTGCTGTCC-5'

	===STEPS===		===STEPS===
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	molecule m;		molecule m;

	m = bdna( "~~gctcatgacaga~~" );		m = bdna( "gctcatgacagg" );
	putpdb( "strand1.pdb", m );		putpdb( "strand1.pdb", m );
	</pre>		</pre>
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	molecule m;		molecule m;

	m = bdna( "~~gctcacgacaga~~" );		m = bdna( "gctcacgacagg" );
	putpdb( "strand2.pdb", m );		putpdb( "strand2.pdb", m );
	</pre>		</pre>
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	===References===		===References===
	# NAB manual (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.460.7407&rep=rep1&type=pdf)		# NAB manual (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.460.7407&rep=rep1&type=pdf)
	# DNA sequence used is a part of DNA sequence used in the paper- Blaine J. Dow, Shuja S. Malik, and Alexander C. Drohat. Defining the role of nucleotide flipping enzyme specificity using 19F NMR. Journal of the American Chemical Society 2019 141 (12), 4952-4962. DOI: 10.1021/jacs.9b00146

Nn320 at 16:15, 29 January 2020

2020-01-29T16:15:07Z

← Older revision		Revision as of 16:15, 29 January 2020
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	===STEPS===		===STEPS===
			----
	=====Creating Watson Crick base paired DNA duplex=====		=====Creating Watson Crick base paired DNA duplex=====
	Load the following modules using		Load the following modules using

Nn320 at 16:13, 29 January 2020

2020-01-29T16:13:07Z

← Older revision		Revision as of 16:13, 29 January 2020
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	Our pdb file containing the mismatched TG base pair is ready to be viewed using vmd :)		Our pdb file containing the mismatched TG base pair is ready to be viewed using vmd :)

	=====References=====		===References===
	# NAB manual (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.460.7407&rep=rep1&type=pdf)		# NAB manual (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.460.7407&rep=rep1&type=pdf)
	# DNA sequence used is a part of DNA sequence used in the paper- Blaine J. Dow, Shuja S. Malik, and Alexander C. Drohat. Defining the role of nucleotide flipping enzyme specificity using 19F NMR. Journal of the American Chemical Society 2019 141 (12), 4952-4962. DOI: 10.1021/jacs.9b00146		# DNA sequence used is a part of DNA sequence used in the paper- Blaine J. Dow, Shuja S. Malik, and Alexander C. Drohat. Defining the role of nucleotide flipping enzyme specificity using 19F NMR. Journal of the American Chemical Society 2019 141 (12), 4952-4962. DOI: 10.1021/jacs.9b00146