Samples: B-form DNA, 6 Atracts and a region of increased flexibility

Features found in this sample CYCLIZE script:
  • Creates a 156nt long B-form DNA.
  • Adds 6 in phase Atracts between positions 25-82.
  • Adds a regions of increased tilt and roll flexibility (9.2 versus 4.842) between positions 101-131.
  • Runs 1 simulation of 1x10^8 whole chains.
    • Notes:
  • If you want to only run multiple calculations, simply change the line that says foreach $repeat (1) to say foreach $repeat (1..10).
  • The value of $cyclize_parameters{whole_chains} can be adjusted to calculate more or less whole chains.
  • Notice the new parameter hash definition for %FLEX and the calls to the "&fill_name" and "&fill_params", which work to add this site of flexibility to a region of the DNA that was originally filled with standard B-form values. The list @flex_positions hold the nt numbers of where the flex site should be located.
    • To obtain this file, highlight the perl script below and copy/paste it into your favorite text editor, or click here for the raw text file (hold the shift key to save to disk). 
    #! /usr/bin/perl -w
# 
require $ENV{'CYCLIZE_HOME'}."lib/cyclize_lib.pl";

# Build the cyclize parameters hash
%cyclize_parameters = (
    "whole_chains"     => 1e8,
    "nrad_stats"       => 1e7,
    "icalcs"           => 100,
    "radial_cutoff"    => 60,
    "axial_cutoff"     => 40,
    "torsional_cutoff" => 36,
    "nkeepers"         => 10,
);

# Set the default values for generating the DNA
$Temp       = 300;
$nnuc       = 156;

# Build the parameter hashes defined below
&build_parameter_hashes; 

# The positions of the A-tracts
@atract_positions = ( 25..30, 36..41, 46..51, 57..62, 67..72, 78..82 );

# Set the position and size of the flexibility site
$flex_start  = 101;
$flex_size  = 30;
@flex_positions = ( $flex_start .. $flex_start+$flex_size );

# Set the flexibility for the %FLEX parameters hash
# This could be set statically in &build_parameter_hashes,
# but this demonstrates that you can adjust the value dynamically.
$flex = 9.2;
$FLEX{tilt_flex} = $flex;
$FLEX{roll_flex} = $flex;

# Create the generic sequence, with nts named "B"
# and fill the sequence with standard Bform parameters
%seq = &create_sequence( B, $nnuc );
%seq = &fill_params( \%seq, \%BDNA );

# Change the name of the nts in the A-tract sites to "A"
# and fill these regions with A-tract parameters
%seq = &fill_name( \%seq, "A", @atract_positions );
%seq = &fill_Atract_params( \%seq, \%Atract, \%Atract_3, \%Atract_5 );

# Create the generic sequence, with nts named "B"
# and fill the sequence with standard Bform parameters
%seq = &fill_name( \%seq, "F", @flex_positions );
%seq = &fill_params( \%seq, \%FLEX, @flex_positions );

for $repeat ( 1 ) {
    &Cyclize( \%seq, \%cyclize_parameters, "flex_example_$repeat" );
}

exit;

############################################################
# build_parameters_hashes
# 
# USAGE: 
# &build_parameter_hashes;
#
# -This subroutine initialize the defaults for the "parameter hashes" used
#  to construct the "sequence hash".  
# -A single parameter hash contains six keys: tilt, tilt_flex, roll,
#  roll_flex, twist and twist_flex.
############################################################
sub build_parameter_hashes {

    #####################################################
    # BDNA site parameter definitions
    $BDNA_tormod         = 2.4e-19; # torsional modulus (erg*cm)
    $BDNA_rpb            = 3.4e-8;  # rise/bp (cm)
    $BDNA_helical_repeat = 10.45;   # helical repeat (bp/360 degrees)

    %BDNA = (
        tilt       => 0,
        roll       => 0,
        twist      => 360/$BDNA_helical_repeat,
        tilt_flex  => 4.842,
        roll_flex  => 4.842,
        twist_flex => sqrt( $BDNA_rpb*$k*$Temp/$BDNA_tormod )*180/$PI,
        dz         => 3.4,
    );

    #####################################################
    # FLEX site parameter definitions
    $FLEX_tormod         = 2.4e-19; # torsional modulus (erg*cm)
    $FLEX_rpb            = 3.4e-8;  # rise/bp (cm)
    $FLEX_helical_repeat = 10.45;   # helical repeat (bp/360 degrees)

    %FLEX = (
        tilt       => 0,
        roll       => 0,
        twist      => 360/$FLEX_helical_repeat,
        tilt_flex  => 9.2,
        roll_flex  => 9.2,
        twist_flex => sqrt( $FLEX_rpb*$k*$Temp/$FLEX_tormod )*180/$PI,
        dz         => 3.4,
    );
    
    #####################################################
    # Atract site parameter definitions
    $Atract_tormod         = 2.4e-19; # torsional modulus (erg*cm)
    $Atract_rpb            = 3.4e-8;  # rise/bp (cm)
    $Atract_helical_repeat = 10.33;   # helical repeat (bp/360 degrees)

    # Default Atract values for middle of Atract region
    %Atract = (
        tilt       => 0,        
        roll       => 0,        
        twist      => 360/$Atract_helical_repeat,
        tilt_flex  => 4.842,
        roll_flex  => 4.842,
        twist_flex => sqrt( $Atract_rpb*$k*$Temp/$Atract_tormod )*180/$PI,
        dz         => 3.4,
    );
    $Atract{min} = 4;       # minimum number of A's in Atract
    $Atract{max} = 6;       # maximum number of A's in Atract

    # Default Atract values for 5' junction of Atract
    %Atract_5 = (
        tilt       => -7.7,
        roll       => 4.6,   
        twist      => 360/$Atract_helical_repeat,
        tilt_flex  => 4.842,
        roll_flex  => 4.842,
        twist_flex => sqrt( $Atract_rpb*$k*$Temp/$Atract_tormod )*180/$PI,
        dz         => 3.4,
    );

    # Default Atract values for 3' junction
    %Atract_3 = (
        tilt       => 9.7,
        roll       => 0,
        twist      => 360/$Atract_helical_repeat,
        tilt_flex  => 4.842,
        roll_flex  => 4.842,
        twist_flex => sqrt( $Atract_rpb*$k*$Temp/$Atract_tormod )*180/$PI,
        dz         => 3.4,
    );
}