Nucleotide sequences for MacDonald FlaB MolecularBeaconFISH

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inmacdonald
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Nucleotide sequences for MacDonald FlaB MolecularBeaconFISH

Post by inmacdonald » Mon 2 Mar 2015 23:09

Borrelia Burgdorferi - 22 mer - DNA Probe [Molecular Beacon] utilized in FISH method to image Borrelia burgdorferi Flagellin B (Fla B) in
Human Solid Tissue and in Blood and Cerebrospinal Fluid:

TGG GAG TTT CTG GTA AGA TTAA

BORRELIA MIYAMOTOI - 30 MER - DNA probe [Molecular Beacon] utilized in FISH method to Image
Borrelia miyamotoi Flagellin B DNa in Human Solid tissue and in Blood and in Cerebrospinal Fluid:

TCA GCC ATA AAT GCT TCC AGA AAT AAT GGC

BLASTn searches will disclose GenBank deposits from all lifeforms on Earth which
match these at the 100% level
which is required for Molecular Beacon type DNA probes to Hybridize with potential DNA and mRNA sites
in target tissues.

These Probe nucleotide sequences were obtained from DNA Sequence Analysis of Borrelia Isolates, as further qualified by exact species.
The 100% matching nucleotides in GenBank deposits will appear at the top of the computer print out.
For a true 100% match with my Burgdorferi FlaB Molecular Beacon DNA/mRNA probe the 100% match must equal 22/22 nucleotides.
For a true 100% nucleotide Match for the Borrelia Miyamotoi Molecular Beacon for Flagelin B, the Molecular Beacon probe must match at 30/30 nucleotides in Blastn searches.

Respectfully,
Alan B. MacDonald MD, Fellow, College of American Pathologists

May 2 2015

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LHCTom
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Re: Nucleotide sequences for MacDonald FlaB MolecularBeaconF

Post by LHCTom » Tue 3 Mar 2015 4:48

I checked your probe sequences and sure enough:
TGG GAG TTT CTG GTA AGA TTAA
Appears quite unique to Borrelia

and
TCA GCC ATA AAT GCT TCC AGA AAT AAT GGC
is unique to miyamotoi.

So I'm curious what you are actually saying. These are good beacons. Were spirochetes found using these? Where?

Was PCR done before using the beacon or was the beacon used alone without PCR amplification?

If done without PCR, how many spirochetes were observed?
The greater the ignorance, the greater the dogmatism.

Attributed to William Osler, 1902

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inmacdonald
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Re: Nucleotide sequences for MacDonald FlaB MolecularBeaconF

Post by inmacdonald » Tue 3 Mar 2015 14:04

FISH method using these Molecular Beacon DNA probes
Have been posted

PREVIOUSLY

ON THIS FORUM

IN THE

MEDICAL CATEGORY


BEST TO READ ALL OF THESE POSTS, WHICH ARE AUTHORED BY ME


AMAZING !

Alan B MacDonald ,MD, Fellow, College of American Pathologists
March 3 2015

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LHCTom
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Re: Nucleotide sequences for MacDonald FlaB MolecularBeaconF

Post by LHCTom » Tue 3 Mar 2015 19:45

A more complete paper describing the use of Molecular Beacon Probes for Lyme testing.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2670302/

and

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890647/

Everyone seems to combine PCR with Molecular Beacons to ID the amplicons.

It seems like a very useful technique but as the spirochete quantity becomes very low, its difficult to distinguish the beacon from noise.
The greater the ignorance, the greater the dogmatism.

Attributed to William Osler, 1902

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LHCTom
Posts: 341
Joined: Mon 22 Oct 2012 4:18

Re: Nucleotide sequences for MacDonald FlaB MolecularBeaconF

Post by LHCTom » Wed 4 Mar 2015 6:35

More interesting research using Molecular Beacons

Sensitive multiplex PCR assay to differentiate Lyme spirochetes and emerging pathogens Anaplasma phagocytophilum and Babesia microti


http://www.biomedcentral.com/1471-2180/13/295
Molecular Beacons . org Publications
http://www.molecular-beacons.org/MB_publications.html
The greater the ignorance, the greater the dogmatism.

Attributed to William Osler, 1902

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