Product info

BHQnova™ Probes are double-quenched hydrolysis probes that exhibit improved quenching and greater signal-to-noise ratio for long probes (>25 bases). These probes have a 5' fluorophore dye, a 3' Black Hole Quencher (BHQ) and an internal nova quencher incorporated between base residues 9 and 10.

When a long probe (>25 bases) design is necessary, such as to achieve a suitable melting temperature (Tm) in an AT-rich target region, the increased distance between the fluorophore and quencher can reduce the quenching efficiency in regular end-labelled probes. In double-quenched BHQnova Probes, the nova quencher is closer to the fluorophore, which increases quenching efficiency. Increased quenching efficiency reduces background fluorescence and improves assay sensitivity.

Key benefits:

  • More efficient quenching: Improved quenching of long probes, such as those designed in AT-rich regions.
  • Higher signal-to-noise ratio: Double-quenched BHQnova probes have lower background fluorescence, resulting in greater signal-to-noise ratios.
  • Increased sensitivity: Improved assay sensitivity in multiplex reactions.
 

Higher signal-to-noise ratio for long probes

For long sequences, double-quenched BHQnova probes quench the fluorophore signal more efficiently than standard end-labelled probes, which results in lower background/baseline fluorescence values. When assay fluorescence is normalised by baseline subtraction, BHQnova probes show a significant improvement in signal response.

bhqplus melting temp

 

qPCR amplification curves comparing a BHQnova probe (red) and a standard end-labelled probe (black) of the same 35-base sequence. The normalised amplification data illustrates the dramatic improvement in signal response.

Select the best dye for your application

5' fluorescent dye

Abs (nm)

Em (nm)

Internal quencher

3' quencher

  FAM 495 520 nova BHQ-1
  TET 521 536 nova BHQ-1
  CAL Fluor Gold 540 522 544 nova BHQ-1
  HEX 535 556 nova BHQ-1
  CAL Fluor Orange 560 538 559 nova BHQ-1

Use the spectral overlay tool to view compatible dyes for your instrument. Learn more

 

Design recommendations for BHQnova Probes

BHQnova probes provide the greatest benefit for probe designs that are 25 bases or longer. For those shorter than 25 bases, a standard, dual labelled BHQ Probe may be suitable.

BHQnova probes contain the internal nova quencher modification by default. When ordering via our online order tool, the nova quencher will automatically be incorporated between the ninth and tenth base upon adding to the shopping cart – there is no need to designate the internal modification within the sequence.

BHQnova probes are perfectly compatible with other probe formats within multiplexed configurations. Barring any sequence interactions, you can combine BHQnova probes with standard BHQ probes or BHQplus™ probes, within the same reaction.

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{{turnAroundDaysProbeName(typeId)}} usually ship in {{turnAroundDays(typeId)}} business days.
  • Oligos for North America, South America, and APAC will be supplied out of our Petaluma, US manufacturing facility while oligos for EMEA will be supplied out of our Lystrup, Denmark manufacturing facility unless you have an agreement in place.
  • Our advertised turnaround time applies to orders received before 12PM for the local manufacturing site. Turnaround time is defined as the time of checkout until shipment.

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You may want to consider ordering an internally quenched probe for sequences 30 bases or longer.
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Are you trying to include RNA bases? RNA bases are not allowed in standard BHQ probes and so the R character will be treated as a DNA wobble instead (A/G). Please use the custom oligo form custom oligo form to order these modifications or click here for help.
Are you trying to include RNA bases? RNA bases are not allowed in BHQnova probes and so the R character will be treated as a DNA wobble instead (A/G). Please click here for help.
Are you trying to include RNA bases? RNA bases are not allowed in standard BHQplus probes and so the R character will be treated as a DNA wobble instead (A/G). Please use the custom oligo form custom oligo form to order these modifications or click here for help.
Are you trying to include RNA bases? RNA bases are not allowed in standard MGB probes and so the R character will be treated as a DNA wobble instead (A/G). Please use the custom oligo form custom oligo form to order these modifications or click here for help.
RNA bases are not allowed in standard Molecular Beacons. Please use the custom oligo form custom oligo form to order these modifications or click here for help.
Inosine modifications are not allowed in standard BHQ probes. Please order on the custom oligo form custom oligo form or click here for help.
Inosine modifications are not allowed in standard Nova probes. Please order on the custom oligo form custom oligo form or click here for help.
An invalid character has been entered into this sequence. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
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Internal modifications are not allowed in standard Molecular Beacons. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
Internal modifications are not allowed in standard BHQplus probes. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
Internal modifications are not allowed in standard MGB probes. For additional assistance, click here for help.
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Inosine modifications must be included in brackets such as [I] or [i].
Internal modifications are not allowed in standard primers. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
No special modifications are allowed in BHQplus® probes and primers. Use the custom oligo order form custom oligo order form to order sequences with specialty modifications or click here for help.
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This oligo contains a number of 'wobbles'. Please consider limiting this to one trinucleotide wobble and one dinucleotide wobble in two different locations or three dinucleotide wobbles in three different locations such that there is a maximum of 6 variants in a single oligonucleotide.
Inosine modifications must be included in brackets such as [I] or [i].
Internal modifications are not allowed in standard primers. Please order this sequence as a custom oligonucleotide custom oligonucleotide or click here for help.
No special modifications are allowed in BHQplus® probes and primers. Use the custom oligo order form custom oligo order form to order sequences with specialty modifications or click here for help.
No special modifications are allowed in MGB probes and primers. Use the custom oligo order form custom oligo order form to order sequences with specialty modifications or click here for help.
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Technical Specs

 BHQnova Probes specifications
Probe length 25 bases or longer
Dyes FAM, TET, CAL Fluor 540, Hex, CAL Fluor 560
Quenchers nova (internal), BHQ-1
Yield Dye dependent (see product listing)
Purification Dual HPLC
Delivery format Dry or in solution (water, TrisHCl, T10E0.1, T10E1)
Quality control MS and UHPLC
Quality standard ISO 9001 or ISO 13485 (enquire for information)
Shelf life 12 months from date of manufacture

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