## TITLE('PCR Primers That Are Efficient and Avoid Mispriming')
## DESCRIPTION
## Select the statement that is TRUE or FALSE about PCR primers that are efficient and avoid mispriming.
## ENDDESCRIPTION
## KEYWORDS('PCR primers that are efficient and avoid mispriming','true/false','multiple choice')
## DBsubject('Laboratory Techniques')
## DBchapter('')
## DBsection('')
## Date('2026-07-12')
## Author('Neil R. Voss')
## Institution('Roosevelt University')
DOCUMENT();
loadMacros(
"PGstandard.pl",
"PGML.pl",
"PGchoicemacros.pl",
"parserRadioButtons.pl",
"PGcourse.pl",
);
TEXT(beginproblem());
$showPartialCorrectAnswers = 1;
#==========================================================
# AUTO-GENERATED GROUPS FROM YAML
#==========================================================
@true_groups = (
[
'the primers are about 18 to 30 nucleotides in length',
],
[
'the primers are complementary to highly conserved regions of the genome',
],
[
'both primers have about the same melting temperature (Tm)',
],
[
q{the primers' sequences do NOT bind to each other to form primer-dimers},
'the primers do NOT have any complementary regions to each other',
],
[
'the ends of the primer sequence must NOT bind to form secondary structures',
],
[
'the percentage of G/C bases in the range of 40% to 60%',
],
[
'the primers have a melting temperature (Tm) in the range of 50°C to 65°C',
],
[
'the primers would ideally have unique sequences that a deficient in 1 of the 4 nucleotides',
],
);
@false_groups = (
[
'the primers are shorter than 10 nucleotides in length',
'the primers are at least 50 nucleotides in length, if NOT longer',
],
[
'the primers are complementary to highly variable regions of the genome',
],
[
'each primer has a unique melting temperature (Tm), one is high and one is low',
],
[
'the primers are rich in A/T bases at the 3′ end to ensure good binding',
],
[
'the primers are mostly complementary to each other',
'the primers can readily bind to form primer-dimers',
],
[
'the ends of each primer are self-complementary to form strong secondary structure',
],
[
'the percentage of G/C bases are less than 30%',
'the percentage of G/C bases are more than 70%',
],
[
'the primers have a melting temperature (Tm) less than 42°C',
'the primers have a melting temperature (Tm) more than 68°C',
],
[
'both primers must always contain all four possible nucleotides',
],
);
#==========================================================
# GLOBAL SETTINGS
#==========================================================
$topic = 'PCR primers that are efficient and avoid mispriming';
my $local_random = PGrandom->new();
$local_random->srand($problemSeed);
my @mode_choices = ("TRUE", "FALSE");
$mode = $mode_choices[$local_random->random(0, $#mode_choices, 1)];
$num_distractors = 4;
#==========================================================
# SELECT GROUP
#==========================================================
my (@selected_group, @opposite_groups);
if ($mode eq "TRUE") {
$group_index = $local_random->random(0, scalar(@true_groups)-1, 1);
@selected_group = @{ $true_groups[$group_index] };
@opposite_groups = @false_groups;
} else {
$group_index = $local_random->random(0, scalar(@false_groups)-1, 1);
@selected_group = @{ $false_groups[$group_index] };
@opposite_groups = @true_groups;
}
#==========================================================
# PICK CORRECT + DISTRACTORS
#==========================================================
my $correct_index = $local_random->random(0, $#selected_group, 1);
$correct = $selected_group[$correct_index];
my @available_group_indices = (0 .. $#opposite_groups);
my @selected_distractor_indices = ();
while (@selected_distractor_indices < $num_distractors && @available_group_indices > 0) {
my $random_index = $local_random->random(0, scalar(@available_group_indices)-1, 1);
push @selected_distractor_indices, splice(@available_group_indices, $random_index, 1);
}
@distractors = ();
foreach my $group_idx (@selected_distractor_indices) {
my @group = @{ $opposite_groups[$group_idx] };
my $distractor_index = $local_random->random(0, $#group, 1);
my $distractor = $group[$distractor_index];
push @distractors, $distractor;
}
@choices = ($correct, @distractors);
#==========================================================
# SHUFFLE CHOICES (SEED-STABLE)
#==========================================================
my @choice_indices = (0 .. $#choices);
my @choice_shuffled = ();
while (@choice_indices) {
my $pick = $local_random->random(0, $#choice_indices, 1);
push @choice_shuffled, splice(@choice_indices, $pick, 1);
}
@choices = @choices[@choice_shuffled];
#==========================================================
# RADIO BUTTONS WITH A/B/C/D/E LABELS
#==========================================================
$rb = RadioButtons(
[@choices],
$correct,
labels => ['A','B','C','D','E'],
displayLabels => 1,
randomize => 0,
separator => '',
);
#==========================================================
# PGML
#==========================================================
BEGIN_PGML
[@ $mode eq "TRUE" ? "Which one of the following statements is TRUE about $topic?" : "Which one of the following statements is FALSE about $topic?" @]*
[_]{$rb}
END_PGML
ENDDOCUMENT();