No. DNA strands only pair head to tail. Look up what a paired DNA strain looks like in a biochemistry text book, the hydrogen bond partners won't align.

Its not possible. Unless you reverse the orientation of one of the strand, like this:

5'ATGGCATT3'

3'TACCGTAA5'

It is seems to me not possible

Thank you guys! I really appreciate it!

And spot on, I should have taken a closer look at the H-bonding sites.

you may find this paper interesting Vlad

Parallel DNA polymerase chain reaction: Synthesis of two

different PCR products from a DNA template [version 1; referees:

2 approved]

Vikash Bhardwaj , Kulbhushan Sharma2

Molecular Biology and Genetics Domain, Lovely Professional University, Punjab, 144411, India

MCS Group, Institute of Nuclear Medicine and Allied Sciences (INMAS), Timarpur, Delhi, 110054, India

Abstract

Conventionally, in a polymerase chain reaction (PCR), oligonucleotide primers

bind to the template DNA in an antiparallel complementary way and the

template DNA is amplified as it is. Here we describe an approach in which the

first primer binds in a parallel complementary orientation to the single-stranded

DNA, leading to synthesis in a parallel direction. Further reactions happened in

a conventional way leading to the synthesis of PCR product having polarity

opposite to the template used. This is the first study showing that synthesis of

DNA can happen also in a parallel direction. We report that from a

single-stranded DNA template, two different but related PCR products can be

synthesized.

Corresponding author: Vikash Bhardwaj ([email protected])

How to cite this article: Bhardwaj V and Sharma K. Parallel DNA polymerase chain reaction: Synthesis of two different PCR products

from a DNA template [version 1; referees: 2 approved] F1000Research 2014, 3:320 (doi: 10.12688/f1000research.5813.1)

Copyright: © 2014 Bhardwaj V and Sharma K. This is an open access article distributed under the terms of the Creative Commons Attribution

Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated

with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).

Grant information: The author(s) declared that no grants were involved in supporting this work.

Competing interests: No competing interests were disclosed.

First published: 31 Dec 2014, 3:320 (doi: 10.12688/f1000research.5813.1)

1 2

1

2

Referee Status:

Invited Referees

version 1

published

31 Dec 2014

1 2

report report

First published: 31 Dec 2014, 3:320 (doi: 10.12688/f1000research.5813.1)

Latest published: 31 Dec 2014, 3:320 (doi: 10.12688/f1000research.5813.1)

Paul I owe you a great deal of thanks (you saved me a lot of head ache).

To anyone else who's looking into it: "parallel DNA" seems to be the best key term to search.

Here's another article:

N. Pattabiraman

Biopolymers vol. 25 issue 9 (1986) pp: 1603-1606 Published by Wiley Subscription Services, Inc., A Wiley Company

DOI: 10.1002/bip.360250903

"Can the double helix be parallel?

INTRODUCTION

Since the proposal of the double helix for DNA by Watson and Crick,’ many investigators have asked the question, “Is the right-handed antiparallel double helix the only structure for nucleic During the last decade, apart from the classical right-handed antiparallel double helix, it has been shown both by theoretical and experimental studies that there are other possible structures for DNA such as left-handed B-DNA and 2-DNA.G-I’ All the structures proposed or obtained by x-ray crystallographic studies on nucleic acids and polynucleotide duplexes are only antiparallel structures with Watson and Crick base-pairing schemes. In this report we ask, “Can the double helix be parallel with the reverse Watson and Crick base-pairing scheme for polynucleotides?’ It may be of interest to mention that there have been x-ray crystal structures for a parallel double-helical structure such as the CPA proflavin complex,’‘ a 2:1 complex of adenosine and proflavin complex,’* and an ApApA ~tructure.’~ There are also proposals for parallel double-helical structure for polynucleotide structures such as poly(AH+) - poly(AHf),’4 poly d(A) - 2 poly d(T),lS poly (G) or poly (I),I6 and 2-substituted poly(A) - ~oly(U).’~ In all the above structures none of the parallel structures formed has the reverse Watson and Crick base pairings. In this report a parallel right-handed double-helical structure with the reverse Watson and Crick AT base pairing as a low-energy model for poly d(A) - poly d(T) is proposed. "

Thanks for that Vlad. The authors of the paper that I sent you are on RG and show the practical application of PCR amplifying a reproducible but "incorrect" amplimer. G quadruplex alsocomes under the unusual base pairing possibilities. It looks like many structures may be possible if the energy can be supplied to get over apparently unlikely pairings. Have fun with it

Paul